And this is why approaching dread pirate squirrels with a "good" alignment can result in conflict. It's not so much "everyone who is evil are buddies", and more "why else would a do-gooder be after me?"
While I haven't actually played that many games with overt morality systems, my expectations are such that "there are bounties on my head and you're a notorious do-gooder" is more explanation than I'd expect from most games in which NPC hostility is dependent upon reputation or morality.
Granted, one might consider that implied in some scenarios, particularly if it's a reputation system like in Fallout New Vegas. In that game, factions kept track of your good and bad behavior separately, and depending on how much you'd done of either, would either think well, neutrally, or poorly of you (with some neutral possibilities suggesting they generally find you very confusing).