A lot of cartoon masterminds and villains are depicted as having very good style (Team Rocket in Pokemon is a good example.) Megamind even mocks the trope. This matches the masterminds of real life who are typically CEOs and fairly attractive (don't tell me Bill Gate's sweaters don't turn you on.)
The simpler bad guys, the henchmen and hoodlums, tend to be ugly because they didn't plan to be bad guys but work out of desperation due to the rest of their lives being a mess.