> Batman is a superhero that operates in darkness and has black clothing, yet people don't think of Batman as the BBEG of their comics, no?
Superman: Literally powered by the light of the sun, boy scout who never breaks the rules, hard-working member of the proletariat.
Batman: Tortured soul with tragic backstory, lawless vigilante, billionaire (regarded as evil in popular media, cf. Lex Luthor).
The darkness in Batman is the adversity the hero has to overcome. It's integral to the story but it isn't pleasant. You can't imagine the young Bruce Wayne wishing for somebody to murder his parents so he can grow up to don a bat suit and punch criminals in dark of night.
And so it is with the other common depictions of darkness in hero types -- an internal struggle, not a desired characteristic in itself.
You can find the odd situation where darkness actually is positively desirable in itself, but not enough to overshadow all of the more common ones where it isn't.