Do you think this could be considered as re-writing history (re: American Indians and National Geographic TV)?

We all know the Europeans killed off virtually all the American Indians and how the government made Hollywood only depict the Indians as the bad guys in all their movies. So I'm watching Nat GO and it's pretty much saying that the Indians died due to disease. So for thousands of years they were healthy and it was only through influenza and small pox that coincided with the Europeans that killed them all off? I'm not buying that. Is this revision of history? Or is it true that's how millions of Indians died, by chance just when the settlers arrived and took over the land.