America wasn't founded in order to take anything from Natives; this was a very unfortunate side affect. Your right, slavery was a stain on America for nearly a century. And there was racial tension against Irish, Jews, Italians ect, just like it is for Muslims in some sectors of society right now.
But these people were still given an opportunity to flourish through their own doing, and many of them have. The Kennedy's are the most obvious example of an Irish American family doing supremely well despite lingering prejudice towards Irish immigrants. Obviously other examples exist.
The Muslim question you bring up at the end is different. The reason people are so scared is that Islamic Law contradicts the notion of freedom. We can and should allow freedom of religion, but not before we ensure that all people are free. And Islamic Law flies in the face of a lot that is presented in our Constitution.