"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." (From BBC)
Hayes, who belongs to the "church" of Scientology, didn't consider bashing other religions to be bigoted behavior. Only his church. This is eerily similar to the frothing-at-the-mouth Muslim freaks who lost control of themselves over the Muhammed cartoons. Anti-semitic cartoons were fine with them, but you publish Muhammed, it's curtains.
A bunch of morons.