Absolutely :) Very convincing, but as per your user-info (should have read that before trying to be smart), I should not expect less of someone with a proper philosophical education and the (as I suppose) accompanying repository of philosophical knowledge ;) The subject of your thesis seems pretty interesting,... ah, I'm digressing ;)
Now, regarding Gods and apples: Because that's how I setup the Gedankenexperiment (and assuming I belong to the majority of people, who are neither blind nor suffering from severe neurological problems), if there was some matter in form of an apple on my desk, I should perceive it. IIRC Kant would say that I have a-priory knowledge of the absence of an apple from my desk.
(I'm afraid I can't argue against that, so let me rephrase the first paragraph until I come up with something useful on how to convince you that comparing religion to an non-existent apple is perfectly fine reasoning.)
[... some minutes passed ...]
No, I think you're right. The problem is that, as you say, an 'apple' is an inherently physical object. Hence there either is one sitting on my desk and I can see it, or I can see that there is none. I can not just bend the definition of an apple at will, so I think I'm stuck here; accordingly, when I say "I believe in the apple on my desk", I am basing my proclaimed belief on a verifieable-false proposition; and much as with false assumptions, from that I can obviously derive anything.
Religion (or other constructs of the mind) don't exist as physical objects (there is no religion-shaped matter), yet they influence and shape (ha!) our world, often even beyond what's possible for a physical object [1].
edit So when I say that I still believe in the apple on the desk even if there is proof of the contrary, I am just acting like an idiot - and that's what's actually influencing/shaping my social relationships ;) end edit
But, one ray of light :) Comparing religion to an apple might not be possible, but I think it's undecidable if comparing God to an apple is: What constitutes God is a matter of belief and hence there is no coherent definition. E.g. some might say there is no physical God, or maybe there is one but not "on our realm of existence" (whatever that means). OTOH, some religious people might even go as far to say that there is a physical heaven and a physical hell, even when presented physical proof of the contrary. So, maybe, there is an apple after all? ;)
[1] I can't resist but to note that, if we were on Pratchett's Discworld, this would be much easier. In that case "the Gods" would probably come knocking on my door for implying that they might not exist.