If a hostile country invaded America tomorrow, took all the best stuff for themselves, and then killed or herded all those who didn't cooperate onto barely habitable chunks of land, how would you feel? If you're the invaders, it's a pretty sweet deal. If you're an American in this scenario, not so much.
It would seem as if the system of native american reservations was begun to separate these people from the white colonialists. Pretty much all that followed was disease and poverty. If the native people are choosing to maintain the system now because they get some benefits that is their right but it does not make the system in its founding moral.
The Native American reservations are poorly managed in terms of keeping people happy, sober, and crime-free. There is a large amount of substance abuse and crime which contribute to a variety of health problems including death. Among the crimes often committed are sexual assault. For this reason the system needs to be revised with better police enforcement and education.