It's hard to say... because even the ending doesn't totally push one side or the other. Most atheists will undeniably say its stating that he doesn't believe in God, but I don't think that's the case. I think he is against "organized religions," not faith or God. It's really an interesting take IMO. People need to look up pantheistic and panenthesitic views on God and Process Reality (process studies). There is more to Christian thought than the naive view most Christians state.
I think Mike is saying that the one truth is that NONE of us TRULY know anything about God, but we have to have that faith, that he seems to be struggling with (and is brought up in other songs...see the end of No Place Like Home.) I wish he would come out and inform us!!!
But ya, I think he is struggling with this himself it seems, and wants to believe, but doesn't want to believe in this man made stuff that has covered up the true meaning (explained above).
Did that make any sense hahaha?!