The difference is not in the religion but the adherent. So far as I'm aware, this individual doesn't even claim to sincerely believe in FSMism. Instead he wants to adopt a phony religion, not sincerely held, as a protest against the perceived faults of other religions.
The key thing about religious beliefs, and about religious faith is that it's not arbitrary. I can't just change what I believe for no reason at all -- I can't just wake up one morning and say "oh, well, I guess I'll be Shinto today." This is why religion needs special protection. Through a bitter series of wars in Europe, we learned that it's best for everyone to let everyone follow their conscience, so that we don't start more wars by trying to restrict or enforce any sincerely held religious creed.
If this guy were actually sincere in believing in the FSM, then I'd say that believe deserves protection (even though FSM-ism was clearly created as satire.) He's not sincere, and that's pretty damn obvious.