Well if it's a public school and they also ban hijab and jesus crosses then he probably doesn't have a case.
the 'Intelligent Design' being taught in science classes, he din't want to be left out, so he express his "religious beliefs" in protest if you will, but he was denied of the same religious expression that the Kansas school was demonstrating in public schools.
By and large, we don't ban either in public schools. I think where he may not have a case is that it would be difficult to support Pastafarianism under freedom of religion in the court system. It was started by atheists as kind of a joke, and it's well known that they don't really worship a Flying Spaghetti Monster. If he could solemnly swear under oath that he sincerely believes in the noodly goodness, he might have a chance.
He could use that classic get out of jail free card the religious use when they are backed into a corner; "that's just the way god (the FSM) done it". He could say the FSM deliberately made atheists start the religion to show how awesome he is. I don't see how they can ban him, so long as they allow other religious dress. The law has no business deciding the validity of a belief, only your rights to practice it. And if rights are afforded to people who, say, believe in a jewish zombie whose flesh they have to consume, then rights have to be afforded to someone who thinks god is pasta. When you look at it, the FSM isn't any more retarded than the rest of the crazy shit these lunatics believe. in fact, it actually makes more sense in most cases.
That's a brilliant strategy, though it looks like he decided to let it go. The Church of the Flying Spaghetti Monster even wrote about it on their site, complaining of religious discrimination. On that post they said they were also having a hard time keeping the server running because of all the traffic, and they were #1 on Digg and Reddit. At least he brought in a lot of publicity, and I'm sure many new converts.