If naturalism is true then human beings can’t have any supernatural insight into deep philosophical matters about meta-physics/ethics, ontology etc. Regular human intelligence is the only tool human beings have to access the truth of these matters.
Moreover, human intelligence evolved with little to no adaptive pressures on deep philosophical matters. (To survive it doesn’t matter nearly so much whether you develop a true metaethical account as it does whether you believe truly about the tiger attacking you.)
Moreover, cognitive psychology has demonstrated that there are many non-rational mechanisms that affect our reasoning. It is quite possible to be mistaken even about why you hold the beliefs you do, let alone be mistaken about the fundamental nature of reality.
Moreover, human intelligence can only work with the limited data at hand. The data pool we have access to is largely determined by the culture and time period we are born into. Worldviews are roughly distributed across geographical regions.
Moreover, deep philosophical matters are recognised to be the most difficult matters for human reason to penetrate anyway. The greatest minds in human history have held radically different views on every imaginable problem within the field. And most people are not “the greatests minds in human history”.
Therefore, the naturalist ought to believe that the reliability of their “deep philosophical cognitive faculties” are very low. While they may be justified in their deep philosophical beliefs, it is highly unlikely any of these are actually true. Any naturalist who steps into the realm of philosophy ought to believe that there is a radically low probability that the findings they come to will actually be true.
This argument is increased in power if Plantinga’s evolutionary argument against naturalism succeeds.