I'm a Catholic. When I was about 8 or so, I really considered the fact that "because my parents had me baptized when I was a baby" should not be the one reason a person may state they are of a particular faith. So I thought a lot about things like the existence of God and Jesus, eternal life and other aspects of Christian religion in general (including, but not exclusive to Catholic ideas). I concluded that I do in fact believe in God, and in Jesus among other things, and that I am perfectly content being a Catholic.
I realize I went a little off track there, but I wanted to premise my post so I don't give the impression of being close-minded.
I think history certainly does play a role in how "legitimate" a religion is, like it or not. When you look at major faiths, they have been around for hundreds or thousands of years. Religions take time to become established- maybe scientology will become mainstream in a 100 years or so, maybe it will fizzle out. There's no telling what would happen as far as I can see. But, in that case, things like the Oprah-couch jumping Tom Cruise being a major supporter, well, that doesn't help it. I think history and the number of followers ultimately are the keys to which religions gain special rights. I think that holds true for granting rights for anything, usually.
I think another principle to look at in terms of how "legitimate" a faith is is how the followers treat others. Now, I totally understand that there have been some very dark and bloody aspects to Catholic history. I'd be naive not to acknowledge that. But, in recent years the church has cleaned up it's act. That helped me stay a Catholic. Recent anti-homosexual comments by Pope Benedict bothered me though, but with things like that I keep in mind: The Catholic Church is comprised of human beings, no human being is perfect, therefore the Catholic Church (or any faith) is not perfect.
I respects all faiths except for devil worship. Being a Christian and being alright with devil worship is like cheering for both the Flames and Oilers.
It's inconcievable, and I personally can't tolerate it.
Except for that, if you tell me you genuinely believe in the flying spaghetti monster, and most of the monster's followers are respectful towards others, then you have just as much a right to practice your religion as I do mine.
That's the thing about faith. If it were absolutely, 100% undeniably certain, we'd call it knowledge. Therefore, there has to be concessions for different schools of thought AKA different religions.
That's my two cents. I hope I contributed something worthwhile!