UPDATE: I've seen the episode now, and I see that Comedy Central censored it, blacking out the few seconds when Muhammad was just standing there, looking normal. Actually, the censored part could have been a joke. You have to read the newspaper to learn that it really was censorship. After the censored part, there's a gloriously uncensored animation, from al Qaeda, depicting Americans and Jesus amid a flurry of turds. Some folks are perturbed at this:
A frequent South Park critic, William Donohue of the anti-defamation group Catholic League, called on Parker and Stone to resign out of principle for being censored.
"The ultimate hypocrite is not Comedy Central — that's their decision not to show the image of Muhammad or not — it's Parker and Stone," he said. "Like little whores, they'll sit there and grab the bucks. They'll sit there and they'll whine and they'll take their shot at Jesus. That's their stock in trade."
Well, the point is that Comedy Central didn't censor the blatant desecration of Jesus, while it censored a depiction of Muhammad just standing there. So clearly, it is responsive to threats of violence, not to nonviolent religious sensitivities. This was the point being made throughout the show, as the character Kyle arged to the TV executive: "Either it's all OK, or none of it is. Do the right thing."
AND: You've got to love the manatees. All the idea balls must be in the tank, available to make into jokes, or they will not work at all. I note that Donohue is demanding that Parker and Stone follow the ethics of the manatee. I think it's enough to admire the manatee, and then continue to press onward and try to get some good work done. Donohue is really exhibiting the ethics of Cartman, who would say what he needed to achieve his real goal, getting the TV show he hates off the air.