The issues you bring up are incredibly complicated. This includes treaties which made Natives citizens, but didn't really ask if we wanted to be citizens. Most American Natives weren't considered citizens until early in the 20th century, and Alaska only became a state in 1959, meaning that Alaska Natives weren't considered until then to be citizens either.
Of course money is involved, but there is also questions of autonomy, land ownership, and whether Natives are to join the Union at all. So it's not just based on a race issue, but issues of sovereignty weigh heavily.