The conquest of north America was largely done by smallpox. As soon as the Europeans arrived, it doomed 95% of the population, who had been spared countless plagues and viruses that swept through Asia, Africa and Europe over the millenia. This fractured many tribes and collapsed their numbers to a point where they had no meaningful polity, maybe a few hundred to a few thousand at most.

Among the remaining tribes and the decimated numbers, many did in fact eventually integrate with Spanish, French, or English settlers, particularly the tribes that allied with them against another rival tribe, such as the Tlaxcalans who aided the Spanish in conquering the Aztecs, and subsequently integrated.

We hear the most and remember the most the tribes which warred the most fiercely (ie Commanche, Apache, Sioux, etc), however, we scarcely remember the tribes they themselves slaughtered, enslaved, and scalped, such as the Crow and Pawnee (who would ally with the US Army) . And some like the Iroquois were generally peaceful and continue to this day.