…if you are a naturalist and think that we have come to be by evolutionary processes, then you will think that the main purpose of our cognitive processes, our mental faculties, is survival and reproductive fitness, not the production of true belief. Evolution doesn't give a rip about whether your beliefs are true. It only cares whether or not your actions are adaptive, whether they contribute to your fitness. From the point of view of evolution together with naturalism, you wouldn't expect that our faculties would be really adjusted to truth or aimed at truth. They would just be aimed at fitness.
But if this is true, if our minds are aimed at mere survival, not at truth, then it's not probable that our minds should be reliable—that is, produce an appropriate preponderance of true over false beliefs; and if that is so, then one who believes both naturalism and evolution should reject the thought that our minds are reliable. But that's a crippling position to be in. Nietzsche is among the people who have suggested this problem. Some contemporary philosophers—Thomas Nagel, for example—have voiced the same worry, and so did Darwin himself.
This is not the first time Plantinga has addressed evolution in Christianity Today. Other articles can be found here.
What I find most interesting about Plantinga’s argument is the way it reduces evolutionary naturalism to it logical end: the deconstruction of the human intellect.
Evolutionary naturalism is the belief that a natural process not guided by any outside personal force produced life in all its complexity. Naturalism is worth attacking on several fronts (see articles here, here and here), but Plantinga may have the best approach.
Without God we are truly lost.
(Other takes on the relevant arguments can be found here and here.)