Several different reasons:
1. In order to be able to do the physical feats we see, they have to be in shape, so they work out and that gives them their bodies.
2. Sex sells. Look at Powergirl. She's famous for her twins. If someone like Mary Jane had acne, coke-bottle glasses, greasy looking frizzy hair and a beer belly, she'd never hook up with anyone in the comics and there wouldn't be that "you've got to save the good looking girl" kind of tension. Plus, as someone mentioned above, there are some people that sadly get off on how say, Rogue, has a rack to Tuesday, so we've got to please those sad little people lol.
3. Its a fantasy. Fantasies have ALWAYS been like this. The wicked witch is always ugly, the princess is always beautiful, the prince is always handsome and cunning, etc. Cinderella isn't obese and Sir Lancelot doesn't have goiters lol. A lot of people try to live out their own lives through fantasies, whether it be films or novels or comics, and attractiveness is one of the major categories of perfection.
4. Character development. If Bruce Wayne was rich and hideous, he wouldn't be the playboy we know him as. Someone like Bruce Banner is generally portrayed as not being a particularly attractive guy, and that easily can contribute to his anger issues.
Yadda yadda yadda. It isn't just a lack of creativity (although some characters definitely could fit into that category).