The indigenous people of Japan are the Ainu, and while the question of "why aren't they more known about" is essentially unanswerable, insofar as the degree of "knowing" is going to depend a lot on the time and place where that question is asked – they will be a lot better "known" on Hokkaido, which is where most of those who identify as such now live, for instance – it's fair to say that a large part of the answer to your question is that they were first marginalised geographically, and then forcibly assimilated into Japanese society over the past 350 or so years by a Japanese state that, curiously enough, derived quite a large part of its "frontier policy" from the example of the actions of the US on its own western frontier. I elaborated on what this assimilation meant, and why it was engaged in, in an earlier response that you can check out here.
I covered these changes and the reasons behind them in writing an essay on the last major Ainu rebellion against Japanese rule, and with apologies for not having time to completely reconfigure that here, because I'm on holiday at present, I'll give that below because it does answer your question and I think the rebellion itself is an interesting and telling one. The original, which is illustrated and has maps, is available here.
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The octogenarian who took on the shogun
There has always been something otherworldly about Hokkaido. It is the most northerly of the four great land masses that make up Japan, and although separated from the mainland, Honshu, by a strait only a few miles wide, the island remains geologically and geographically distinct. Spiked with mountains, thick with forests, and never more than sparsely populated, it has a stark and wintry beauty that sets it apart from the more temperate landscapes to the south.
Hokkaido is such a familiar feature on maps of Japan that it is easy to forget what a recent addition it is to both the nation and the state. It does not appear in Japanese chronicles until around 1450, and was not formally incorporated into greater Japan until 1869. As late as 1650, the island was known as “Ezo,” and was a distant frontier zone, only tenuously controlled from Edo (modern Tokyo). Even in the 1740s, Tessa Morris-Suzuki notes, maps of the region still showed it “disappearing over the horizon and petering out in a splash of unconvincing islands.” And while it seems always to have possessed a small population of Japanese hunters and merchants, Hokkaido was home to, and for the most part run by, a significantly larger group of indigenous tribes known collectively as the Ainu.
It was not until the 1660s that Japan asserted its dominance over Hokkaido, and when it did it was as a result of one of the most self-evidently doomed rebellions known to history. Shakushain’s revolt, they called it, after the octogenerian Ainu chief who led it, pitting 30,000 or so ill-organized tribesmen against a nation of 25 million, and stone age military technology against the modern firearms of Japan. He lost, of course; just one Japanese soldier died fighting the rebels, and Shakushain himself was ruthlessly assassinated as soon as a peace treaty was signed. But while the Ainu suffered in the short term–enduring an influx of Japanese onto their island, and ever harsher terms of trade–it no longer seems quite so clear who the real victors were in the long run. Today, Shakushain has become an inspiration to new generations of Ainu nationalists.
The roots of Shakushain’s revolt lie buried in Japan’s prehistory. The Ainu–the word means “most humanly beings”–are a people of obscure origins whose closest links are with the natives of Siberia. Yet at some point in the distant past there must have been wars between the Ainu and the Japanese, which the Ainu lost. There is evidence, in the form of place-names, that their range once extended deep into the mainland, perhaps even as far south as the latitude of Tokyo itself–but by the first years of the 17th century they were confined to Hokkaido and the Kuril chain, and found themselves under increasing pressure to yield what remained of their commerce to the merchants and the warriors of Japan.
As for the causes of Shakushain’s revolt: There can be no doubt that trade–specifically, Japan’s determination to ensure it got the best of every deal made in Hokkaido–was the trigger. But as tensions on the island rose, threats were made by the outnumbered local Japanese that amounted to promises of genocide. For that reason, the main dispute between historians who study this little-noticed episode revolves around a single question: Is the Ainu’s struggle best seen as an economic or a racial conflict–or even as a war of independence?
It does not help that the centuries separating the development of an Ainu culture in Hokkaido after 660 from Shakushain’s rebellion in 1669 are only sketchily illuminated, more so by anthropology and archaeology than by the historian’s craft. But it is now generally agreed that the Ainu moshir–”Ainu-land”–remained culturally distinct throughout this period. The Ainu were hunters, not gatherers; they fished for salmon and tracked bear and deer. Religious life centered on shamans and an annual bear festival, during which (it was believed) the divine spirit of a captured bear was freed by sacrificing it. The main exports of Ainu-land were hawks, bears’ livers and dried fish, which were exchanged for metalware, lacquer bowls, sake and the rice that was so hard to grow in northern latitudes. Meanwhile, the Japanese presence on Hokkaido remained almost entirely confined to a tiny enclave on the island’s southernmost promontory.
It was only after 1600 that relations between the Ainu and the Japanese reached a tipping point, and Japan became distinctly the senior partner in both diplomacy and trade. The change coincided with momentous events in Honshu. The Tokugawa shogunate, established in 1603, restored peace, stability and unity to the country after more than a century of war and civil war; the new ruling family shifted the capital to Edo (now Tokyo), thoroughly reorganized the feudal system, and suppressed Christianity. The mid-1630s saw the introduction of the policy of sakoku–which may be roughly translated as “locking the country”–under which practically all trade with the outside world was prohibited, foreigners were expelled from Japan, and others were forbidden, on pain of death, from entering imperial territory. The Japanese were not permitted to leave, and trade with the outside world was permitted only through four “gateways.” One of these was Nagasaki, where Chinese vessels were cautiously admitted and the Dutch were permitted to unload a handful of vessels annually on an artificial island in the harbor. Another, on Tsushima, conducted business with Korea; a third was located in the Ryukyu Islands. The fourth gateway was the Japanese enclave on Hokkaido, where trade was permitted with Ainu-land.
Sakoku, the historian Donald Keene notes, exacerbated a Japanese tendency
to see foreigners (and particularly Europeans) as a special variety of goblin that bore only superficial resemblance to a normal human being. The usual name given to the Dutch was komo or “red hairs,” a name intended more to suggest a demonic being than to describe the actual coloring of the foreigners’ hair. The Portuguese had also at one time been declared by the shogunate to possess “cat’s eyes, huge noses, red hair and shrike’s tongues.”
The Ainu, likewise, were objects of suspicion. They were typically shorter and stockier than most Japanese, and had considerably more body hair. Ainu men cultivated long beards, a most un-Japanese trait. They were also not disposed to yield to increasing pressure from the south. There was fighting between the Ainu and the Japanese in 1456-57 (an outbreak known as “Koshamain’s rebellion“), from 1512 until 1515, and again in 1528-31 and 1643. In each case, the issue was trade. And each time, the Ainu lost.
This growing imbalance of power accelerated after 1600. By then, the Japanese had firearms in the shape of matchlock muskets, which they had acquired from the Portuguese, while the Ainu still depended on spears and bows and arrows. Japan had also become a unified state at a time when the people of Hokkaido still lived in warring tribal groupings, lacking (Shinʼichirō Takakura notes) an economy large enough to support any “permanent political organization”–or, indeed, a standing army. The largest Ainu polity of the 17th century was only 300 people strong.
The shogun’s authority, admittedly, was not absolute. Rather, it was exercised through several hundred daimyo–feudal lords who lived in castles, collected taxes and maintained order in their districts with the help of samurai. For the most part, the daimyo maintained a sort of semi-independence that became more entrenched the further from the capital they were based. Certainly Japan’s representatives in the northernmost parts of Honshu, the Matsumae clan, were reluctant to invite interference from Edo, and a missionary who visited their territory in 1618 was curtly informed that “Matsumae is not Japan.”
As /u/mikedash pointed out, "knowing" depends entirely on the time and place where that question is asked. The answers given thus far all focus on middle-late era of Japan's history. Let me offer up an early history perspective because the "natives" of Japan.
To start, we need to look at what "native" really means. The deep roots of Japan's population goes back about 35,000 years ago to the Upper Paleolithic era even as the cultural and ethnic character we think of today only goes back to the Yayoi (弥生) period about 900 BC. The oldest known human bones in Japan are from cave sites in the Ryukyu 28-34,0000 years ago, with hand axes and knives in the now Tokyo area similarly dated. Following those super early timesframes, we see new bladed artifacts emerge from northern Hokkaido to southern Kyushu some 20,000 years ago. What's interesting is that those artifacts, as C. Melvin Aikens puts it, are "clearly related to [similar artifacts] made across Eurasia, from the Atlantic to the Pacific." It was during that time about 20,000 years ago that people became numerous and varied in rich environments of seashores, bays, rivers, etc that the archipelago provided. This fits with the hunting and gathering societies across the globe, with fish being an abundant resource- though numerous excavations of encampments show traps for game like wild boar.
The Jomon ((縄文) period begins about 14,000 BC. Keep in mind this was all happening towards the end of the last glacial period, which allowed for migrations from the warmer climates homo sapiens while land bridges still existed (for example, Bali was connected to Indonesia via the Sundaland). Warming temperatures gave way to lush forests and grasslands. It's no surprise that homo sapiens began to flourish and form communities around the available natural resources. By the early Jomon (5-6,000 years ago), pithouses with excavated floors and perishable superstructures (ie, non-permanent walls) became plentiful, then large communal storehouses for food were found in the middle Jomon some 4,000 years ago, and by the final Jomon era about 2,000 years ago, communities in northn Japan persisted with elaborate ceramics the period is known for along with artistic, social, and ceremonial activities. There is even evidence of trade and interaction between communities around Tokyo Bay, not to mention Kyoto-Osaka, Okayama, and northern Kyushu.
Here's where things get interesting when we talk about "native" in Japan. Multiple genetic studies confirm genetic ancestry between the early Paleothic "natives" to Japan and the mainland. This was before the glacial melting which further isolated the islands. Are these the "natives" we speak of- peoples who settled 20,000 years ago? Or is it more complicated?
I argue with other historians that it's more complicated. Immigration played an important role in the peopling of Japan. The Yayoi period, and the Kofun (古墳) period that grew out of it, is inseparably linked to an earlier emergence of agriculture and Bronze Age society in Korea. The Middle Neolithic Jeulmun (즐문 or 櫛文) culture of the Seoul region- which was strikingly similar in its fundamentals (and even the cord-marking of its pottery) to the hunting/fishing/gathering Jomon tradition of Japan- began to incorporate the cultivation of millet and other continental plants into its local version of the broad-spectrum hunting/gathering economies that grew in parallel all around the Sea of Japan about 5,500 years ago. Around 1,500 BC, those cord-marked pots had effectively vanished, which historians refer to as the Mumun (민무늬, lit. "without cord-marking") period. As prosperity and population grew, together with more cultivated crops, Mumun households with strong community leadership began to emerge. Continued growth menat tnter-community competition for resources. This ultimately led to emigration across the Korean Strait to northern Kyushu and southern Honshu by 400 BC at the latest.
This is the point where "native" begins to get confusing. The skeletal features of Kyushu natives found in Late Jomon graves are most similar to those of the contemporary ainu of northern Japan and Ryukyuians of far southern Japan, who are clearly descended from the native Jomon population. The modern Japanese population is recognizably different from both the Jōmon and Korean populations, and unmistakably the product of intermarriage between Korean emigrants and Jomon Japanese natives. As alluded to earlier, these biological relationships have been documented over many decades in a substantial literature based on various forms of morphological analysis, and more recently confirmed by genetically based research on a set of contemporary populations that compared twenty different genetically determined blood group, red cell enzyme, and serum protein systems.
Most importantly, it needs to be understood that at this point in time (begininng of the Yayoi), "Japan" as a state did not exist. I've written about the emergence of Japan's statehood in other posts . Briefly summarized, tribal competition, ritual, trade, technology, together with a mixture of immigration and cultural appropriation from the mainland led to the Yamato (大和) period and what we might call "Japan." Consolidation of power under a paramount (Tenno 天皇) plays a key role in the "what happened with the natives" story.
By the beginning of "Japan" we have two distinct "natives" to the country: one from the indigenous Jomon hunter–gatherers and the other from East Asian rice farmers who first migrated into the archipelago about 2,300 years ago (Yayoi). Genetic data supports this model in two main regards. First, the genetic profile of the mainland Japanese reveals a strong signature of admixture, best modeled as a mixture of ainu-related ancestry and continental East Asians. Second, the ainu are genetically closer to the Ryukyuians from the southernmost islands of the Japan than to the mainland Japanese. This suggests that inhabitants of the northern and southernmost parts of the archipelago were genetically most isolated from the incoming farmers who first arrived in the central part of the archipelago.
Both "natives" end up being victims of politics in this story. As intermarriage and generational families grew, so did they expand to other areas of Honshu. Communities and kingdoms pop up in the northen lands on Honshu. Ainu and emishi (毛人 or 蝦夷) intermix as this takes place. And these communities do not wish to submit to the Central Court of the new state of Japan. This ties into the origins of the shogunate which I also wrote about previously. The main title of shogun (将軍) is ultimately a derivative of the seii taishogun (征夷大将軍). Chinjufu shogun (鎮守府将軍 aka chinju shogun) can also found as a separate title referring to the "Military General" under the seii-taishogun.
The northeastern third of Honshu was still beyond the court's control in the 8th century AD. This area, sometimes referred to as michi no oku (道の奥, literally "deep in the road" but more like "the deep interior of the land"), was inhabited by emishi/ainu. What would become known as the provinces of Mutsu and Dewa were beyond the court's control, were codified in the ritsuryo as being "outside the land that has been transformed" (kegai 化外), meaning outside the area "tranformed by" the court's control. The Nihon Shoki has tales of emishi/ainu as "eastern savages" of "violent disposition" though modern scholarship knows the tales are different than reality. Still, that was the perception of the court, driven by cultural and geographical differences.
As I explain in that post on the shogun, the court expanded into those northern territories which disrupted the "native" way of life. They tried to assimilate tribes through diplomacy- with varying degrees of success. But ultimately it turned violent, with multiple campaigns in the 8th century taking place to subdue the barbarians. Hence the seii taishogun title. The last court action took place in 811 AD when they declared the emishi as pacified, though reality was different. Politics were the same back then as they are today!
Ultimately, Paleolithic natives intermixed with immigrants across Honshu and Kyushu, and communities that didn't bow to the Court in the Nara and Heian periods were subjugated/assimilated through diplomacy and violanece. Hokkaido is a bit of a different beast because it wasn't really part of Japan until more modern times. Back in the early days, the island of Ezo (蝦夷) was an extremity, a place for banishment that was considered outside the realm of the nation. Bruce Batten in his book To The Ends Of Japan discusses this and includes various maps showing what was considered "Japan" during the 8th, 13th, and 18th centuries. Note that in none of those images is Hokkaido considered part of the country. Hence why I keep it separate from all the discussion above.
Hopefully you find this helps address the early "native" situation a little bit.
Sources-
Thank you, that was a great summary.