Dawkin's main concern seems to be that religion promotes a feelings-based, blind adherence to a few ancient texts and eschews rationally examining and testing our beliefs (which is what scientists and atheists do). Since religious believers are so sure that they are right, and because they have such blind faith in authority, they can be persuaded easily by their religious leaders to do all sorts of horrible things like blowing up mosques and killing abortion doctors.
Dawkin's argument could be interpreted one of two ways: either as a plug for science as the only means of knowing, or as a more complex argument centered around testability and verifiability of beliefs, with science as a prime example. I think the most charitable read of Dawkins is the latter. The first interpretation is called logical positivism, and it died as soon as people realized it was self-refuting (the statement “only scientific facts count as knowledge” can't be scientifically verified). I assume Dawkins knows this.
On the other hand, to the extent that his objections weren't based on science they were sloppy, unoriginal, and completely ignored 2,000 years of first-rate Christian scholarship. If all it takes to defeat Christianity is quoting a few of the bloodier passages of the Old Testament and making an offhand comment about how God must have been trying to “impress Himself” by sending Jesus to die for our sins (since he could have just forgiven them without all that nonsense about an atoning sacrifice), then we're in trouble. But this sort of critique represents the opposite of the critical thinking that Dawkins prides himself on. He relies instead on proof-texting and one-liners for most of his arguments, and makes no effort whatsoever to ineract with the texts he quotes out of context.
The usually very secular Guardian has an interesting commentary on Dawkin's documentary here:
There's an aggrieved frustration [by atheists] that they've been short-changed by history; we were supposed to be all atheist rationalists by now. Secularisation was supposed to be an inextricable part of progress. Even more grating, what secularisation there has been is accompanied by the growth of weird irrationalities from crystals to ley lines. As GK Chesterton pointed out, the problem when people don't believe in God is not that they believe nothing, it is that they believe anything.This is right on. Dawkins does indeed complain that he expected us all to be atheists by now. He seems very concerned that people could be so irrational as to still believe in religion in the 21st century. Of course, the possibility that the flaw is in his analysis of religion, not in religion itself, is not something he considers.