It's an obnoxious question, but Neutral Milk Hotel has enough complexity and authenticity going for it to give it a little weight. For the most it's not about Church or religion, it's about faith and affirmation and connectivity and openness, and all that great Milch-ian romantic existentialism. The pain of the past being transformed into the future tense of joy. And so forth.
What people fail to understand is that the church is a political institution. Religion a sub-genre of art. Faith is the willingness to give oneself over to artistic invention. God is metaphor; the organizing principle around which a community can form.