I never really cared about the hero's costume matching whatever animal it's supposed to be-- I mean, if we're going to really get into it, Spidey should have six extra eyes and the web-shooters in his butt, Wolverine and Batman should both be brown, and Black Canary should replace her fishnets with feathers.

Without going into color theory (which I never actually studied), it seems to be that in comics, generally speaking good guys wear primary colors, bad guys wear secondary colors.  It's about the closest thing to team uniforms they get, and works really well as visual shorthand, especially in splash pages with tons of characters displayed.

Plus, I mean, people just respond more strongly to them than more natural colors-- there's a reason everything from first-person shooters to national politics divide opposing sides up into Red Team vs. Blue Team.  You want something that catches the eye immediately and provokes a response?  Primary colors FTW.