In short: Columbian Exchange. Europeans unknowingly introduced a number of highly contagious diseases to Americas, including smallpox, which devastated the native populations of the western hemisphere. By the time Spanish, French, and English settlers started to make their way into the mainland, the native civilizations were either destroyed completely, i.e. the Mississippian culture, or disrupted to the point at which no effective resistance to European incursions could be mounted in time, i.e. Incan Empire. Along with killing off some 80-90% of the population, the epidemics also disrupted the ties between the survivors, resulting in several internal conflicts. In the end, there just weren't too many Native Americans left to dominate, and the land, cultivated by the generations of the locals was too good to pass up, even in the face of the resistance put up by the survivors.