Well the point is, they don't. It's one thing to make fun of people, and culture. I'm not offended if someone makes fun of TV evangelists, or nuns, etc. However, when they do hold up our Lord God as something vile and someone to be reviled, then there is something deeply perverse and evil going on. For you to defend them says more than you think about your spiritual development.
For the love of pete, it's a TV show. Family Guy's digs on Catholicism offend me far more than South Park's do (mainly because FG is ignorant, whereas SP knows what it's talking about.) But you don't see me calling for them to take off any episodes of it.
If you truly think South Park hates God, the Catholic Church, etc, then go watch the episode dealing with the pedophilia scandal.