Beliefnet recently posted an interview with Richard Dawkins called "The Problem with God."  It is a fascinating discussion, and I highly recommend reading the whole thing.  Briefly, I find the following problems in Dawkins' responses:

1) Overlooking epistemological issues.  He says, "I would want them to believe whatever evidence leads them to; I would want them to look at the evidence, judge it on its merits, not accept things because of internal revelation or faith, but purely on the basis of evidence."  Is this possible?  Dawkins fails to acknowledge the difficulty of how one interprets data and evidence.  He is being far too simplistic here.

2) Inconsistent appeal to authority.  While we cannot accept things by revelation or faith, he admits that he accepts things from other scientists: "Not everybody can evaluate all evidence; we can’t evaluate the evidence for quantum physics. So it does have to be a certain amount of taking things on trust. I have to take what physicists say on trust, for example, because I'm a biologist. But science [has] a system of appraisal, of peer review, so that I trust the physics community to get their act together in a way that I know from the inside."  So, Dawkins still accepts some things as true because others tell him that they are true.  These truth claims are supported by an appeal to authority (in this case, scientific expertise).  Amazingly, in the next sentence, he says, "I wish people would put their trust in evidence, not in faith, revelation, tradition, or authority."  Does he not see the inconsistency here?  The difference is not one between authority and evidence; the difference is one of between type(s) of authority.

3) A misunderstanding of science.  When asked, "There are intelligent people who have been taught good science and evolution, and who may choose to believe in something religious that may seem to fly in the face of science. What do you make of that?"  He replies: "It’s certainly hard to know what to make of it. I think it’s a betrayal of science. I think they have a religious agenda which, for reasons best known to themselves, they elevate above science."  Here, he fails to recognize the philosophical basis of science and falsely equates science with naturalism and materialism. 

4) A theological naiveness.  Answering a question on Intelligent Design, he says, " ... it doesn’t explain where the designer comes from. If they’re going to emphasize the statistical improbability of biological organs—'these are so complicated, how could they have evolved?'--well, if they’re so complicated, how could they possibly have been designed? Because the designer would have to be even more complicated."  All one has to do is to differentiate between contingent and necessary (incontingent) beings.  This kind of question makes me wonder how much he reads or interacts with those who differ with him.

Again, these are just some quick thoughts.  But they do point to some fundamental flaws in the thinking of atheists like Dawkins.  I only wish that the interviewer was willing to challenge Dawkins more on some of his answers!