I think that there were unfortunate choices that, when combined, led to the final product being fairly easily perceived as racist.
I've said before that, if they had bumpy foreheads or wore the clothes from, say, The Hunted, then I think the accusations of racism would have much less footing.
Exactly. Racist? nah. bad taste, bad choices yes.
As an American Indian, I can certainly complain about that episode with Wesley in season seven. My biggest complaints were the writers and actors saying "We're doing an Indian episode!" Awesome guys when are you doing a Jew episode? (Ferengi aside) and the dialogue "What are you going to do about your Indians Picard!" Oh they arn't colonists?*
And don't get me started on Chakotay.
*I do want to say that awareness has grown leaps and bounds since that ep and also that like Code of Honor, it isn't racist, just bad choices and a little ignorance.