In short, the difference between belief in God and belief in the Flying Spaghetti Monster is this:
Belief in God is rational and supported by good reasons, and belief in the Flying Spaghetti Monster is irrational and not supported by any good reasons. Bobby Henderson simply begs the question (commits a logical fallacy) when he says that there are no good reasons for belief in God. Despite his claim to the contrary, Christianity is a rationally defensible religion. There are difficult questions that we must ask ourselves as Christians, but the fact that there are difficult questions is not grounds for dismissing Christianity. As believers, our pursuit of answers to our own deep-seated spiritual questions draws us further into the intellectual richness of the Christian faith.