"what is the rationale for criticizing all the bad things America did to Native Americans to achieve its current greatness"
It is the United States that did the evil to the Native Americans, and any stick will do to beat on her. Because, as we all know, the ends justify the means and the United States is standing squarely in the way of the Utopian paradise.
On a less satirical note... I will sometimes talk with the resident indian in my house (my wife prefers the term indian rather than native american, since my whole family are "native Americans") about this topic. She likes to learn about her cultural heritage (Creek Nation) and thinks there was alot of evil done to the indians by us "white folk". She also realizes that it was not a one way street and that there was more than enough bad stuff to go around on both sides. She also notes that the indian tribes did not live in perfect harmony with each other as they had their own share of wars. It's interesting to listen to her dad (1/2 Creek) talk about some of the other tribes. But while it's interesting to learn her heritage, she does not desire to live like the women in that heritage normally lived. When push comes to shove, she is actually quite thankful for that group of dead-white-guys known as the Founding Fathers. She thinks liberty, private property, rule of law, limited government, and Christianity are all Good Things. Or as Muhammad Ali said after returning from the "Rumble in the Jungle" when asked what he thought of Africa, "I'm sure glad grandaddy got on that boat." This doesn't excuse the evils of yesteryear, but it does add a healthy perspective to hopefully prevent similar evils in the future.
Hey, at least our egg-breaking actually ended with an omelet.