It stems from people that need to feel smarter than everyone else, so they clump anything that has to do with religion into a bible-thumping-child-molesting-creationist-believing morons. The problem is the worst of the bunch is what the Internet actually sees, and then what the Internet sees defines the group.
I can tell you that I am Catholic, I am very private about it, I don't shove my beliefs in other people's faces, if someone doesn't believe in what I believe in I respect that, and there have been no sex scandals or any other types of scandals in our parish in recent history. In fact, our pastor makes $25000/year, and he donates most of it back to the church to pay for programs to educate kids in music/language, upgrade nursing homes, feed the homeless, and setup education programs for orphans.
I don't believe in a lot of the dogma of the Catholic church, and at this point I'm not even sure God exists at all as we now have reasonable explanations of everything back to the creation of the universe, but I can say that he church does so much good that I'm glad to be a part of it.