HawkProbably because it passed under their radar. It wasn't a hot topic back then and the reasoning behind his appearance was to create representation for every mayor religion.
What I find funny about the South Park situation is that they showed Mohammad clearly and in his entirety in an earlier episode back in the show's fifth season. He was your average guy in a turban, but he had the ability to shoot fire for some reason.
Now, they're in trouble for showing a mascot bear costume and implying that Mohammad was inside it. They didn't even show him!
I guess it's possible for Muslims to simply be angry that Mohammad is a character in an often tasteless cartoon, but it makes you wonder what they were doing eight years ago when Mohammad first made an appearance.
When the Mohammad cartoons were posted in that Danish newspaper, it caused a huge uproar and a wild debate about freedom of speech. South Park made fun of that event by hinting that they were gonna show Mohammad again but didn't do it in the end. Now that they did it again, they were in the radar, the topic was still alive and thus it became controversial. They were also aware of what they were doing, this time.
There's a difference between unwittingly doing something offensive and doing it intentionally. When I was a small kid I heard of a curse word that was derogatory towards Jewish people. I had no idea what it meant but all I knew was that it was bad word. I used it on my peers in order to insult them, not knowing the meaning, just like I would have done with words like “idiot” or “jerk”. Eventually I was informed of the meaning. If I had used the word from that point onward, it would have been considerably worse of me to do so, wouldn't you agree?