One consequence of a naturalistic worldview (i.e. the view that the natural world is all there is) is that atheism would be very likely to be true, and if atheism is very likely to be true then materialism (i.e. the view that everything in the universe reduces ultimately to matter and energy, there are no immaterial substances like mind or soul), would be very likely to be true.
Now, materialism entails that every thought we have is solely the product of chemical reactions in the brain, but if that's the case what reason do we have for thinking that any of our thoughts are actually true? Why think that neurochemical reactions would or could produce true thoughts?
How, after all, could atoms swirling around on a neuron be expected to reliably produce a truth?
And if, given materialism, our thoughts can't be trusted to be true, what confidence can a materialist have for thinking that materialism, naturalism and atheism are true?
It would seem that naturalism, if we follow it consistently to its logical conclusion, leads to complete epistemological skepticism, including skepticism about the truth of naturalism.
The only escape from this problem for the naturalist is simply to decide to exercise blind faith in his neurochemistry to lead him to trustworthy beliefs, but ironically blind faith is one of the things he criticizes religious people for having.