I don't think Superman is hated any more then any other comic book character, I just think more people have heard of him. I think Wolverine is overrated, but there are several people who think he should be the only thing on the shelf. I guess metal claws that come out of your hands is a cooler power then being able to fly or shoot lasers out of your eyes for some people.
The hatred for Superman in my opinion stems more from the idea that he is a block of wood that has no personality, bearing in mind that most of these people making this accusation don't read him on a regular basis; assuming they ever did. Superman is seen as the "establishment", the "man", the father figure always telling you to eat your vegetables. Our pop culture frowns on conformity and Superman is seen as the poster child for "how your supposed to be". Other people see him as perfect and like the idea of flawed heroes. Me, it just depends on what I'm in the mood for. I think you can still have a universe with a god-like superman and a flawed Peter Parker at the same time.