Basic Trope: All beautiful characters in a work are good, and all good characters in a work are beautiful.
Straight: Alice, Bob, and Charlie, the three heroes, are very attractive, while all the villains are somewhat unattractive.
Exaggerated: Alice, Bob, and Charlie are heartstoppingly gorgeous, and the villains are all hideous, twisted monsters.
Downplayed: Good characters always stop short of being ugly even though higher amounts of beauty don't mean anything. Alice is attractive, Bob is average , and Charlie is merely plain.
Alice, Bob, and Charlie are shapeshifters who didn't want to take ugly forms, for fear of frightening small children and weakening their cause, and the villains are a species of inhuman, deformed beasts.
The characters can detect whether someone is good or evil, manifest in the form of attractiveness.
Alternately, the villains were cursed for their evil-ness to look like monsters, whereas the heroes were blessed for their goodness.
The cast consist of supernatural creatures whose outside appearance reflects how they are on the inside.
The gods grant Holy Magic only to the good, and only Holy Magic can heal, so the villains' appearance stems from their massive scarring.
There's a deity in the show that makes people look ugly or attractive depending on what path they take in life.
Zig Zagged: Heroes Alice, Bob, and Charlie are all beautiful, when it's revealed that Charlie was The Mole. He shifts into his hideous true form shortly afterward. Then, villainous but attractive Daryl shows up, but he's actually working for the heroes. As soon as Daryl returns to Alice and Bob's side, though, he changes outfits and stops looking attractive. This is shortly resolved by a makeover from Alice. Then, we meet a new Hero, Evelyn, who's rather ugly...
Averted: Some beautiful characters are heroes, but some are evil, and there are some average or ugly people on both sides.
A line of action figures based on the series is going to be sold, so all the heroes are good-looking to increase their appeal. Additionally, the villains are ugly so that people will like their action figures for the "monstrous" look.
The people learn to judge people by their behavior and not their appearances.
Played For Laughs: Alice is Obviously Evil but hot. Bob repeatably points out her evil to no avail. "She's too pretty to be evil."
Played For Drama: The reason for the attractive mutants avoiding the vicious unceasing torment from society. The unattractive ones had enough of thislong ago. The best they can manage are Well Intentioned Extremists who seek to end the viscous of vanity of society. Even if it means destroying anything in the way of their purge of the cruel and vain idiots from power.
A really good-looking person wants you to go back to Beauty Equals Goodness. You know you can trust her and that she isn't trying to lead you into a trap, because she's beautiful.