Evolution does not work with Naturalism

Alvin Plantinga has said in an article in Christianity Today that Evolution does not work if your a Naturalist or Materialist or a high-octane atheist (those three are kinda clumped together in the article). Have a read of the article and see if I have missed something in his argument:

Evolution is about species adapting and it doesn't care if it produces true or correct reasoning, just as long as it works in reality. This then therefore means that if you have evolved you can not trust your own faculties or reasoning to be true, and so you can not trust your reasoning about evolution (or any other idea) as been true. Your ideas/beliefs may work, but in all likely hood may well be false.

This is an interesting argument, but I'm not sure animals really pass down their belief system to their next generation. I would think that a belief that alines with reality is by definition true (I mean, what is truth except something that is real?) and since ideas and beliefs change much faster than a species is meant to adapt (like many times in a life span, regardless of parents), wouldn't it be possible for animals (and us) to work out what is true from adapting/changing our ideas to that which works in reality...

Now I am not agreeing with Naturalism, Materialism, "high-octane" atheism or even if evolution is true or not, I'm just not seeing Plantinga's argument. Maybe I am missing something (which is also quite possibly true).

You can read a good discussion of this article on Victor Reppert's blog here.