Cruise has had to deal with rumours and jokes regarding his sexuality all his career. (Whether he really is gay or not isn't the point.) The fact is that being perceived as homosexual hurts him in his career as a leading man and the types of roles that is suited for.
Isn't it possible that the guy is just fed up a bit with yet another parody involving his sexuality? Wouldn't YOU also feel a bit upset. Sure it comes with the territory of being a hollywood actor but these folks do have feelings.
Then if it weren't bad enough, the same parody also makes fun of his religion. As wacky as we might objectively view it to be, to HIM he is sincere and his (religion) is important to him.
Yes, we all should just laugh about the whole thing and he would hopefully laugh with us - just as we ask minorities to laugh at ethnic jokes, or husbands and fathers to laugh at "dumb dad" or "boyfriend" jokes and women to laugh at "dumb blonde" or "wife or girlfriend jokes." Religion, being such an important cultural aspect, has long been an accepted as fair game and a source for humor. So in some sense Cruise and other Scientologists should consider it a compliment that they are now in the same club as Irish Catholics and Middle-American Protestants, Jews and Jehovah's Witnesses.
Most of the time we laugh. But humor, like beauty, is always in the eyes of the beholder. If a person doesn't laugh at what others think is funny, we might say they don't get it, or as in the article, label them "humorless." Yet, sometimes what others find to be very funny (Andrew Dice Clay, Andy Warhol, Eddie Murphy, Chris Rock, etc.) is considered quite offensive to some. When this is the case, we don't begrudge them if they walk out of the performance, or boycott or protest. That is their right and option.
So Cruise (if such "insider information" is accurate) threatens to bail out of any publicity for MI3. [I wonder whether such info is accurate however, as most players have contract provisions locking them into a certain amount of publicity commitment; and also, not doing publicity for MI3 would only hurt the movie (and his own pocket) not South Park or Comedy Central.].
The guy is upset, he is sick of being portrayed as a homo and to add insult to injury, his sincerely held religiious beliefs are made fun of. Are we really surprised that he might be upset. I know that I probably would be after a certain point.
Humorless? Maybe so. But irrational or abnormal? Probably not.