Neither the FBI nor the BIA have been friendly to Native Americans.
I'm not as knowledgeable as to how AIM was received by tribal members but I do know the tribal leaders and tribal police were seen as no more than agents of the BIA and the government who helped perpetuate the appalling conditions on the reservation.
I did see a lot of things I didn't like. There was a artificial air of reviving the ancient ways. There were talks about the sacredness of the land no more than thirty feet from an old truck rusting in the creek. There was a sign taped to the door of the trailer that served as AIM's headquarters in Porcupine that read, women who are menstruating may not enter.
After the peyote ceremony in the sweat lodge (which was sleeping bags thrown over a structure of sticks) the leader of the ceremony asked for a virgin to step forward to lead the group into the hills to conclude the ceremony. No one stepped forward. One of the women I came with from FOR was a nun so I looked at her. After a moment, she muttered "shit" and stepped forward.
Overall it struck me as a self-conscious and aggressive reclamation of identity. The friction with established leaders probably wasn't that much different from the reaction to the Panthers in their community a few years earlier. The FBI helped destroy them as well.
As to why we stayed in Porcupine, I don't think it was a safety issue, it was a matter of distrust. Not that I can blame them. they had taken a bold step against the government and there was a lot on the line.
Still, flaws and all, I favor them over the FBI and its tactics. By far.