I don't think it was because of native resistance. While there were border disputes during Taira Masakado's time in the 10th century with the Japanese pushing northward, it wasn't native resistance. The Japanese held an absolute extermination policy towards the Ainu, and Ainu populations were barely existent by that time. Resistance from Japanese expansion northward came from other groups that I'm not informed of. Another reason would be the climate and geography of Hokkaido. With only about 25% of Japan consisting of arable land, much of this land is in Honshu. Only recently (in historical terms) has Hokkaido seen intensive agriculture with newer technology. Hokkaido simply has a climate that wasn't ideal for growing food up until the modern era. Hokkaido is also extremely mountainous, another reason the Japanese had not bothered to settle there until much later in their history. Japan Emerging, edited by Karl Friday is a good, recent work from many contributing Japanese scholars on Japanese history up until the Meiji Restorations. If you're interested in more, that would be a great place to start.

Your question is actually much more complicated than it first appears. Essentially Japanese agriculture was based in labor intensive rice cultivation best suited to honshu, kyushu, and shikoku. Rice was used to pay taxes and was measured in koku. In the Tokagawa period Hokkaido was given to a Japanese daimyo who traded extensively with local Ainu for seal furs and other commodities. See Brett Walker's book [Conquest of Ainu Lands] (http://www.ucpress.edu/book.php?isbn=9780520248342) Ainu changed from a hunter gather society to one based on trade with the Japanese for essential goods like rice, sake, and cooking pots. Japan was rarely an "Empire" in the European sense. The Tokagawa was a warlord society with many daimyo controlled individual areas under the shogun, but "colonization" in your sense of the word refers to later Imperialistic developments of the Meiji Era such as Taiwan, Korea, and evenually Manchuria.

Jumping in for a tangenital question.

What makes the Ainu aboriginals, but not the Japanese? As far as I am aware, the Japanese have been on their islands for a very, very long time. Shouldn't they be considered "natives" by now? This thought corsses my mind every time I hear of aboriginal groups in places that I already associate with a deeply historically rooted population, like the aboriginals in northern Scandinavia.

That is actually a pretty good question, and, I want to admit right from the beginning, I cannot provide an answer. But what I find noteworthy is that the colonization of Hokkaido/Ezo-chi was suggested several times from at least the early 18th century on.

Russian ships were appearing on the shores of the Kuriles and Ezo at that time, and these news were alarming to Shogunate officials. We have record of Kudō Heisuke (1734-1800) of Sendai han requesting the Shogunate to colonize Ezo to develop the island's "vast mineral resources". Military strategist Hayashi Shihei (1738-1793) was well aware of the Russian advances as well, and suggested that Japan be prepared in case of an actual attack. And then there is Honda Toshiaki's (1744-1821) quite strange proposition of the Shogunate transferring its seat of power to Kamtchatka in order to achieve world domination.

After Adam Laxman's expedition to Japan in 1792, who wanted to get access to Japanese goods for trade, the Shogunate got increasingly interested in such ideas. It had Ezo surveyed and maps crafted, and took over the Matsumae domain /u/kenjutsudude spoke of in 1802. Several incidents occured during the following years, but then Napoleon drew the Russians' focus of attention away from Japan.

This was just a quick sketch - I only have John Whitney Hall's "Japan. From Prehistory to Modern Times" right here, and it's quite old, but nevertheless an incredibly important book, and I'd still recommend it to anyone interested in the history of Japan.

EDIT: Formatting, forgot a few words.