That sports illustrated poll was about names, not mascots. I think that's what the NCAA is getting at. Personally, someone who dresses in traditional native american garb ala Chief Illinawek of the University of Illinois is much more tasteful than the old Cleveland Indians logo of a grinning cartoonish indian.
And in the relm of names, Seminoles and Illini are not bad. However, like the article mentioned, something like Redmen, or our own Redskins can be seen as offensive. To use a white example, Celtics and Fighting Irish or just Irish are good. But if the nickname highlighted a sterotype or was something like the Micks, that would be bad.