edit: despite his not fitting into the thread title's description, I'd lean towards Geralt's treatment in the Witcher series being typical of many present-day minorities as well. Celebrated/scorned for his magical powers (fast-twitch muscle fiber!), numerous assumptions made about him based on his background, a great deal of unease directed his way by the hoi polloi (how many times have I been spit at in this game? seriously)...there are a lot of parallels. Anyways.
Then Kain and Raziel from Legacy of Kain also fit that bill. Last of their respective kinds, one a vampire and the other a soul-eating wraith, persecuted and slaughtered by the Sarafan Inquisitors.