An important thing to remember is that Hokkaido couldn't really be considered a part of "Japan" (as we know it today) until the Edo period. It was considered barbarian country by the people of Japan, full of "nasty and primitive" Emishi tribesmen ethnically distinct from the more "civilized" Yamato peoples. In fact, the Emishi people actually ranged as far down as northern Honshu and it wasn't until very late in Japanese history that the area wasn't considered their territory--although it was around the 8th century that the Yamato people are said to have established political control over them, perhaps similar to the relationship between Gallic people and Rome. Prominent people in the area may have considered themselves ethnically Emishi or Yamato, as a part of the Yamato political system or completely seperate from it (a different issue altogether), or sometimes even changing their positions. When the Emishi and Yamato came into conflict, whether you consider these conflicts wars or rebellions depends on your own opinion on the complex and shifting relationship between these groups and sociopolitical systems.

It was right before the Edo period (the Azuchi-Momoyama period) in the late 16th century that the Matsumae Clan was given the area on the peninsula of Hokkaido closest to Honshu as a domain and ordered to protect Japan from the Emishi barbarians. When the Shogunate forces were crushed in the Boshin War, leading to the Meiji Restoration in the mid-to-late 19th century, the last holdouts fled to what was considered no-mans-land--i.e. Hokkaido--and established a new political entity called the Republic of Ezo for half a year before being destroyed by Imperial forces.

This should give you an idea of how Hokkaido was viewed by the Yamato people even at this late period.

Although many contemporary Japanese people would be shocked to hear it, Japan as we know it today could be considered an invention of the Meiji Restoration in response both to internal political pressure to create a unified national identity and to competitive pressure from more technologically and economically advanced countries outside Japan's borders.

It wasn't until after this that Hokkaido could firmly be considered Japanese, but soon after Imperial rule was firmly established nationwide, the Meiji government pumped money into Hokkaido as a natural breaker against Russian interests in Pacific expansion. It was only at this point that Hokkaido gained any significant population, and has thus only been growing for about 150 years, which is not much when compared to the rest of Japan. Add in the difficult climate, the mountainous geography, and the universal trend to empty out the countryside for the city, especially in Japan's case the "big" cities like Tokyo and Osaka, (and Hokkaido has almost always been mostly countryside) and you have a recipe for a lower population.