One of the great dangers of brain research today is that as we find the "explanation" for things, we will conclude they are just illusions and not real.

Well, the thing is, we're pretty sure at this point then that everything is "an illusion", by this standard. Religious experience, love, red, pain, it's all just an illusion brought on by neurons firing in certain patterns, right? Moving into the computer realm, the text box I am typing this into is an illusion brought on by clever programming, as is the browser. It's not an isolated series of claims of illusoriness, you need to consider the whole of them at once, including not just the politically popular ones (religion), but everything that argument makes sense for (red, mathematics, scary).

I submit to you that this view, while popular, is silly. How can everything be an illusion? That stretches the meaning of "illusion" beyond sensibility. I propose to you that the "illusion" is in fact the real thing, and what you considered reality was in fact an illusion brought on by your ignorance of how things truly work. Finding a neural explanation for an experience does not make it illusory, it merely brings it into the fold of things you partially understand, displacing your previous ignorant ideas about what is "real".

Failing to take this view is, IMHO, extraordinarily dangerous to yourself.

This text box is not an illusion. It is a text box in every way that matters. I send it keystrokes, it puts up text, you read it later. What more do you want? Red is not an illusion. It impinges upon my eyes, I see it and process in certain characteristic manners, all of which are every bit as real as anything else.

Higher levels of organization are not "illusions" merely because they are not atomic. My car is made of nuts and bolts and fabric and metal, and it is those things, profoundly, but it is also a car. My brain and self is made of neurons and glia and blood flow and individual firings, but it is also my self, nevertheless. My text box is no less real for being built twenty layers deep on various more atomic APIs.

To apply this directly to a contentious point, establishing the neural location of religious experiences does prove or disprove them any more than establishing the neural locations of "pain" proves pain isn't real. To disprove a worldview, you need to use logic of the form "Given your worldview, this fact about the world conflicts", and "I found your religious experiences in the brain" doesn't fit that mould. Christians, Muslims, and other religions with creator gods will claim that the creator god put the circuits there because they tap something real. Hindus may not claim a creator god put it there (I know less about Hinduism), but they will still claim it is there because it taps something real. And so on, for many religions.

I'm not saying this disproves the atheistic, Darwinistic view of religion the "I found the neurons" discovery engenders for such people. I'm saying it doesn't disprove most religions to any greater extent, either; it's basically null evidence on that front.

(And heck, while I'm making controversial statements, may I also add that IMHO this viewpoint very nicely harmonizes the traditionally disparate "Western" and "Eastern" views of the world, and that they not only need not be at loggerheads but actually fuse into something quite nice.)