The rumours of Bowie being a racist stem from his flirtation with fascism around 1974. Setting aside the "Victoria Station Nazi Salute" thing, which is so ambiguous it's actually funny, David did go on record at least twice stating his admiration for Adolf Hitler. He's subsequently refuted that he feels that way, but it *WAS* said and reported by journalists. Some of the more die-hard Bowie fans feel that he should be forgiven for that, as he was gakked out of his head on Class A's at the time. Fascism doesn't necessarily = racism, but that is the source of some long standing rumours.
Anybody who really believes Bowie is a racist or a fascist is crazy. I do believe that he took way too many drugs during the thin white duke days though and probably can't remember half of the garbage he spouted.