I dislike Superman for the same reasons, but admittedly I don't really know much of the character as I never really read DC comics as opposed to Marvel.
For me, my dislike comes from all the utilities his different abilities have, frozen breath, eye beams, x-ray, incredible powerful super strength, resistance, apparently some versions of Superman are also supposed to be a genius too. If your version of Superman has all these abilities, how do you deal with that? I felt like (and I may be very likely wrong, as I said, I don't read DC comics) That the kryptonite weakness was invented because when they thought of the character they couldn't think of a credible way he would lose in a fight, so a tangible weakness had to be invented for him. Also I guess on top of that, he is (once again, from the material I have seem him) too much of a "boyscout" so that just makes him boring for me.
Then again I have been told Superman isn't really all that much about him being super strong, but just more about the character knowing he is from another world and living with how people react to him.
As for why people complain more about him than other heroes who are as, or even more broken, in terms of abilities. I guess is because Superman is pretty much the face of DC so MORE people know about him as opposed to some more obscure comic characters like Fantomex.