Oddly enough, it was something that I was thinking about when my friends and I were talking about Dungeons & Dragons, the pen & paper RPGs. My buddy came up with a good point: the majority of scenarios in D&D seem to revolve around racially motivated home invasions. i.e. They are goblins, and they are evil. My party and I will enter their lair and exterminate them and take their stuff. Heck, the evil "Dark Elves" are black, and that always made me uncomfortable.
I'm not saying that D&D is racist, but it does show the kind of subtle way fuzzy thinking and lack of social insight creeps its way into our cultural vocabulary...in differing cultures, color is intimately tied to emotion. In Western culture you get things like green with envy, red with rage, etc. Black and the darker colors have always had negative connotations.
Personally, I don't think we'll see many overt titles that put you in the place of say a Concentration Camp officer or a machete carrying Hutu, except among the fringe elements that do those awful, race-baiting FPS games. However, I do believe that if people don't continue to challenge preconceived notions, the subtle forms of stereotyping and racism will go on bleeding into video games as you can see today. Arab and Muslims in general are convenient targets these days, and a good portion of modern "combat" games involve taking down droves of "terrorists". Asians (in Western produced games) seem to find themselves constantly as the typical martial artist/mystic/gangster/doctor (although I wish I did have ninja-like skills, I certainly am not much of an assassin)...most of the stereotyping comes into being through voice acting.
Racial "profiling" is not anything that will be entirely erased, and preconceptions will continue to find their way into our forms of entertainment. I just don't think, at this time, we should be excessively alarmed about the possibility of a mainstream title allowing you to play as Nathan Bedford Forrest (the founder of the Ku Klux Klan).