In short, suppression and eradication.
The Protestants of the early United States tended to avoid marrying and continuing the bloodlines of Native Americans due to obvious racial tension and prejudice against them. Native Americans were eradicated on a larger scale in North America rather than South America, so there would be a greater amount of Natives there. (This is because of a more complex and somehow tolerant society in the South) However, there were obviously the mestizos. While there was reproduction between white people and natives, it was typically a result of harassment or an uncommon desire to start a family.
In summary, the amount of Native descendants in the United States is significantly lower now than centuries before because of endless eradication and little amounts of pure-blood Native Americans being born.