Exactly. It's racist because the PTB (obviously mostly middle-aged white men) think its enough to have "minority" characters but don't feel obligated to portray minorities outside of safe, generic white-male assigned stereotypes. Far too often, the inclusion of minories in tv shows by the majority is made to help the majority feel like they're being open-minded by watching a tv show. The focus shifts from equality and inclusion to mollification and self-congratulation. Instead of having Chakotay as the token "Indigenous", they could and should have given him a tribe from the very outset and stuck to the culture and customs of that particular tribe but they COULDN'T BE BOTHERED and that's racist.
Using an actual tribe opens a can of worms. Don't get me wrong I do believe that a dose of reality would have been the right thing to do, made a much stronger story. Using real history makes things harder anytime they needed to add a fictional element, because then you need to be true to history and pay respect to it. It would have been nice, but I'm not tuning into Star Trek to learn actual history or physics.
This is no different with any of the other characters. Picard is some French dude with a winery and Riker is apparently a tough guy from Alaska. It is paper thin for everybody. Screwing up actual history or misrepresenting an actual tribe would be more offensive to me.
Chakotay is one of the few where they actually bother give a backstory. His backstory is rather lazy and bad but this isn't a documentary, they made stuff up on the spot. Frankly his backstory with his dad is better than other characters. It is easy to say it's racist because it's written by white people though.