Unfortunately, what else do they know? It would have to be forced integration to get them back with society.
That is part of it, but Indians face different challenges than other minorities. They have some amount of self-rule & sovereignty on the reservations such that the more traditional natives don't want to leave, despite the conditions.
As has been mentioned, it's a complex issue. Too many make this a "good Indian, bad Caucasian" issue, which oversimplifies the problem and creates problems of its own. Most don't realize that during the 19th century there was a major movement among whites to treat Indians better. Many white teachers went to reservation schools because they wanted to help, not because they were uptight Victorian prigs who wanted to beat the inferior culture from them. The problem in those cases was more ignorance than belligerence.
The same applies to any case where a teacher of one race teaches children of another race. I've heard white teachers talk of the struggles they have teaching Latinos, even when they want to do a good job.
Unfortunately, it's something which is common to many First Nation groups. The causes are complex and relate to treatment in the past and in the present. I don't think there's a quick fix.
True, but it goes even further than that. The Puritan character of the American church has also caused problems for Catholics, Orthodox, and Lutherans. There is still some bitterness among American Lutherans about the way they were treated during WWI & WWII. At the same time, and even though I'm Lutheran, I understand the fear of that time. It's hard even for the best-intentioned to get it right.
As such, I agree with an Indian I heard interviewed on NPR. The interviewer asked if he preferred to be called Indian or Native American. He replied that he was neither. Both of those were labels created by and applied by whites. He preferred to use the name of his people from his native tongue. But, he added, he didn't expect whites to know that name just as he didn't know if, beyond being white, his interviewer was English, French, or German, etc. As long as people treated him with respect and good intentions, it was easy to accept being called Indian, Native American, or whatever word they came up with.