I feel that this quote by Matt Stone (in regards to Isaac Hayes departure from the show) is truly epic and is very applicable in the cases of people all-of-a-sudden becoming offended with the show.
"In 10 years and over 150 episodes of South Park, Isaac never had a problem with the show making fun of Christians, Muslim, Mormons or Jews. He got a sudden case of religious sensitivity when it was his religion featured on the show. We never heard a peep out of Isaac in any way until we did Scientology. He wants a different standard for religions other than his own, and to me, that is where intolerance and bigotry begin."
I can understand that people could get offended, I don't understand why people who think it's okay to make fun of figures of other faiths would get offended. To me, it's intolerant for one to say it's funny when the show makes fun of Jesus, Mahatma Gandhi and ManBearPig, but extremely offensive when they go for Muhammad. Of course, this does not apply to people who think the entire show is offensive.