I think this is a great topic. It's an issue that I've always struggled with. I've gone back and forth myself, and I'd love to hear what other people think on this issue.
Here's a followup question: if you think churches should be taxed exempt because of the first amendment, are gun manufacturers tax exempt by the second amendment?
EDIT: Considering I don't even take a position in this post, I'm not sure what the downvoter could possibly be objecting to.