I was agnostic for a good many years. Ironically I now think that the biggest reason for faithlessness is a lack of balls - to put it bluntly - within the intellectual community. I don't support religiousness, or any dogmatic faith, really, although I consider myself Christian - but this is more because it's the easiest way for me to contextualize my faith in something bigger than 'this' into the framework of reality I've grown up with, not because I would elevate the Bible or what's contained in it above anyone else's faith... as long as they have faith. That goes directly against Abrahamic beliefs, I know, but screw it. The Bible itself is full of contradictions, and my own personal tendency is to accept the fact that human beings have been mucking around with it for over 2000 years, not to mention ripping entire segments out (cough cough, Martin Luther), so while I feel connected to the basic message, I think accepting any of it literally - or accepting ANYONE else's interpretation of it, barring a message from God Himself - would be ludicrous and putting more faith in men than God.
As far as the idea that critical thinking tends to weaken religious indoctrination, I don't find that surprising at all. Religious people are those who claim to have faith because they want a social comfort zone, which is pretty much the opposite of what 'faith' is really about, at least when you start talking about faith around other people. I would say a faithful person would probably basically accept that conversations about faith are going to be uncomfortable for them, but would feel impelled to take part in them anyway regardless of that.
Anyway, on to my point: having been agnostic for a long time, I think part of the problem with the atheist/agnostic lean of the intellectual community is that it is just as biased, if not more so, than any given religious community. Religion is dying out because it is becoming less and less socially comfortable to be religious, not because any specific tenets of any given religion have been 'disproved'. There is a HUGE amount of social pressure within most groups of intelligent people to mock faith and faithfulness in general, and because most people are weak-willed (and please, don't debate THAT point with me - look how successful religion was before the advent of the industrial age and it becomes obvious), they will succumb to social pressure rather than looking inward and trying to actually analyze and examine their own thoughts about the scarier and least known-about parts of whatever this thing we call 'life' is.