I just wrote a huge post covering all your major points, and I just lost the damn thing. I'm really, really upset now. :( I'll try and summarize what I though was my best point below, and put the horror behind me.
"I know it's all my brain responding to auditory stimuli. Should I stop listening to music then?"
"That's what I think it's wrong with atheism, atheists keep shouting the mantra that religion is only inside our brains, and theists reply that that fact alone doesn't make any difference."
Emotions, love, laughter, etcetera, are all constructs of the human mind. They never lose their potency, regardless. If someone tells me a good joke, I laugh regardless of whether or not I know that said laughter is just a function of the limbic area of my brain. Relgion is different. It DOES lose its importance when it is acknowledged that it is a human construct. Why? Because emotions claim no hold over outside creation. They realize their limitations. No one believes that concepts like humor and happiness would exist outside of life, because they are an integral part of life and life alone.
Religion, on the other hand, claims to describe the very nature of the universe. If it truly exists in our heads, that makes it wrong. Truth is not subjective. If we weren't here, atoms would still exist. Electricity would still exist. Planets would still exist. There is a truth outside of the human experience, and it can be described. Truth is not a function of consciousness, and religion, you seem to say, IS. Rationalism describes what definitely is. Theology and philosophy describe what might be. Which is more reliable for finding truth?
If you're walking along a dirt road, and there's a rock directly in your path, yet you believe with all your might that the rock isn't there; if you honestly and entirely are sure that the road ahead is clear, will you still stub your toe when you kick it?
I repeat: TRUTH IS NOT SUBJECTIVE.