Dennett's Dilemma -- to give it a name -- is quite reasonable if you grant him his underlying naturalistic and scientistic (not scientific)assumptions, namely, that there is exactly one world, the physical world, and that (future if not contemporary) natural science provides the only knowledge of it. On these assumptions, there simply is nothing that is not physical in nature. Therefore, if God exists, then God is physical in nature. But since no enlightened person can believe that a physical God exists, the only option a sophisticated theist can have is to so sophisticate and refine his conception of God as to drain it of all meaning. And thus, to fill out Dennett's line of thought in my own way, one ends up with pablum such as Tillich's talk of God as one "ultimate concern." If God is identified as the object of one's ultimate concern, then of course God, strictly speaking, does not exist. Dennett and I wll surely agree on this point.
But why should we accept naturalism and scientism? It is unfortunately necessary to repeat that naturalism and scientism are not scientific but philosophical doctrines with all the rights, privileges, and liabilities pertaining thereunto. Among these liabilities, of course, is a lack of empirical verifiability. Naturalism and scientism cannot be supported scientifically. For example, we know vastly more than Descartes (1596-1650) did about the brain, but we are no closer than he was to a solution of the mind-body problem. Neuroscience will undoubtedly teach us more and more about the brain, but it takes a breathtaking lack of philosophical sophistication — or else ideologically induced blindness — to think that knowing more and more about the physical properties of a lump of matter will teach us anything about consciousness, the unity of consciousness, self-conciousness, intentionality, and the rest.
This is not the place to repeat the many arguments against naturalism. Suffice it to say that a very strong case can be brought against it, a case that renders its rejection reasonable. Dennett's reliance on it is thus dogmatic and uncompelling.
It's a fair point. Science comes with its own religioust trappings, valid or not, e.g., the constant chanting of falsifiability, or third-person verifiability. Dennett stresses that religion is unfairly protected from skepticism. Could be. But the scientific mythos and its philosophical underpinnings deserve just as much skepticism, if we're to be fair.
People advocating skepticism usually mean: "Express skepticism towards those things I don't believe in, but not towards those things I do believe in." Hence, if you doubt religion, you're a free-thinking bright, but if you doubt science, you're a ridiculous solipsist.