I did. None of the teams was the "bad" team. But everyone wanted to be Cowboy, cause they got the cool guns :P
Maybe "bad" isn't quite correct, since children aren't as likely to see them as good/bad.
But I've played a few times, and seen others play it, and it's always been playing it as if the Indian has stolen a woman, or raided your cows, or whatnot.
The cowboy/indian game is a minor point, really. Out of personal experience, it's always been that if anyone was ever bad, and therefore deserved the fight, it was the Indian, not the Cowboy.
Another good example.
I definitely won't deny that the British (and other exploratory countries) have made countless indigenous races of people out to be savages.
And most of them aren't alive anymore to even defend themselves.