Chakotay's subordinate role could just as easily be interpreted as a preference to showcase the female captain and female power. A sexual liberation from fictional tropes. I can't say that watching the series I ever saw a "Tonto", or a character that should be thought less of because of his race. Sure, they wasted many artistic opportunities with his character and it's a damned shame. But he was portrayed as a good character, a hero, a man worthy of emulation.
However, he's only worthy of emulation because he capitulates. Would he be so worthy of emulation if he'd been the captain's equal?
BTW, Tonto wasn't really a fool--he was simply the sidekick. And that's what Chakotay is--Janeway's sidekick.
However Teya brings up an important issue, which is very true - that majority cultures tend to make other cultures peripheral in their stories. And in extreme cases, caricature them as villains and fools, which still goes on in this day, believe me, I see it every day.
But cultural self-absorption, and active racism are not necessarily the same thing.
Actually, I don't think the writing of the character was "racist"--in the strict definition of the term. And I've never used the word to describe Voyager's writing.
It was, however, culturally insensitive. And that could have been remedied easily--by simply utilizing sources available to them.
Now, yes, I view this through the lens of an indigenous woman. So did the writer of the essay that was linked to.
exodus views it through the lens of a man of color.
Others, as has been said, view it through different lenses.
Perhaps my lens is wrong. Perhaps I should get rid of that huge chip on my shoulder and accept that a passive servant is the best representative of my people I can expect out of Hollywood. After all, he's not a villain and he's not a fool. That's better than it used to be--why complain? Maybe it's the best we can get.
Maybe I'm being foolish to want to see Indians played as human beings, rather than cartoons.
And, well, if that means that other people think that's who we really are, well what's the problem? After all, the victors write the history, so who the hell cares who we really are?