Whether one is talking about materialism or naturalism, what counts against them is the same: Self-referential inconsistency, arbitrary self-exemption, self-reduction, and criterial assumptions.
As Wilbur Urban argued with regard to naturalism, if the naturalist thesis is taken as an account of all knowledge, then that thesis itself cannot claim to be true. It can only claim to be a product of its own posited universal explanatory factors.
According to naturalism, the truth of the naturalist account itself, like every other item of knowledge, is merely the function of the adjustment of the organism to its environment. Therefore, the truth of the naturalist account has no more importance than any other adjustment except for its possible survival value.
But the general principle applies to all reductive, fixed-factor, universal theories. There's simply no way for those theories themselves to break out of their respective explaining/determining factors and be considered true in addition to being themselves merely the product of those factors.
Key questions to ask are: When do we get to add the label "true" on top of the explanatory/determining factors of these kinds of reductive theories? What's the criteria? And how can materialists and naturalists criticize theism, when theism too is just as legitimately explained and determined by those same factors as those theories which specify them?
Urban's writings were a major influence on Stuart Hackett (who Norman Geisler once told me personally was in his opinion the world's greatest living Christian philosopher), and reading just the first few mind-halting pages of Language and Reality will clearly show why---as well as blow your mind.
The Intelligible World. Allen and Unwin, 1929.
Language and Reality. Allen and Unwin, 1939.
Beyond Realism and Idealism. Allen and Unwin, 1949.
Humanity and Deity. Allen and Unwin, 1951.