This is exactly why this issue is never really given any credence, outside of a few isolated cases. Sports teams are generally named after something fierce, tough and hard to defeat, although sometimes simply after something native to that area. This is exactly why so many schools historically used Indians as mascots. It definitely is honoring them. You dont choose a mascot name to make yourself look weak or to make fun of yourself or something else. Here in Tallahasseee, the "Seminole" name is actually BACKED by the Florida Seminole Tribe. There are about three or four Seminoles not affiliated with the tribe that protest here and there, but are generally ignored. The people that bitch about this do so because there is nothing else to bitch about at that time.
My junior high was called The Horned Toads. It was embarrassing.