I started to type this last night, but then the power went out and I gave up. In the interim, the conversation has moved on somewhat, but I'll share it anyway.
I took several philosophy courses with the Jesuits at Georgetown. They were rather specific courses (not philosophy 101), such as 19th century French philosophy and the like, and while the courses were secular you won't be surprised to find out that Catholic philosophers were rather highly represented in our readings. In contrast, I also took a course there by a moderately famous visiting Chinese philosopher on Chinese philosophy (and that was a Chinese 101 course).
As far as actual reasoning goes, I detected no difference between the rationality, meaning the ability to present and dissect arguments, nor in the ability to generate counterarguments (thinking on the hoof, so to speak). Anyone in any of the courses would consider the lecturer rational on those grounds.
The real problem comes in at empericism. Rationality is not enough - it will never, ever prove that I have a tree in my front yard (in general). Rationality must always be combined with empiricism to arrive at anything resembling the truth.
I consider the Jesuits to be a pretty extreme (refined?) example of people who use very refined arguments to make their points, without really getting to the nub of it - is it real? A very subtle argument hinged on the Argument from Design still suffers from two major flaws (at least): nodirect evidence, and the evaluation of circumstantial evidence. By that I mean, roughly (too early in the day to get too bogged down in this) that we have no overwhelming, unarguable evidence for God, and so the argument breaks down to how much weight we put on each piece of the argument, how likely each piece is, how the probabilities of each sums togethers, etc.
As an aside, I spent some time in the humanities writing and reviewing at a professional level, and they really do think probabilities sum. Meaning if I present an argument that has a 50% chance of being write, assume that is true, and then present a follow on that is 50% right (If billy went to the store (50%), and he stole the milk (50%), then...), the result is nearly likely to be true. Improbabilities strung on improbability = certainty. Uh, no.
You generally don't see the same problem with the Jesuit philosophers and the like, but they still suffer from the same problem in a more subtle form. Argument on top of argument on top of argument, etc. All without looking back at the root: is this true?
I sympathise with this, as I know I do similar things in my daily life. For instance I invest heavily in oil/gas, and was just reading the peak 200 oil thread, where somebody posted an article from the Financial Times. The article's conclusion agreed with what I think, and more importantly what would be financially rewarding for me, and I found myself nodding along unsceptically. Then I caught myself.
So, the end result is I don't really know what to think about some of the more subtle thinkers about religion. Surely the "oh man, it'll all so connected somehow, there's gotta be something out there" thinkers aren't being all that rational. But what about somebody who has really thought about things and weighs evidence differently than I do, and that aren't dogmatic about things (open to new ideas, don't hold the bible is the literal truth). Are they really being unrational, or just evaluating key points differently? If I had to guess, having no training in human psychology (and being rational, I have to recognize I'm now doing what I accuse the Jesuits of doing, reasoning without emperical evidence), some people have a bit of a blind spot about the fundamental question of God's existance, leading them to overweight very circumstantial evidence (the universe looks 'designed', they 'feel' God inside of them, etc).
With that said, read this thread, and see how just about every post is doing the same thing - arguing without really solid emperical evidence. Rationality without incontravertable evidence. Ask yourself - did you feel rational while typing it? Is your argument more solid than the Jesuits? I would say probably a bit more solid, but that you (and I) have more in common than in difference.
I don't know; religion to me is just so obviously a set of fairy tales that I can't get beyond that. When someone starts to say "I think.." my mind is screaming "EVIDENCE" before they can get the rest of the sentence out, practically. So it's very hard to put myself in the place of somebody for whom that doesn't seem so screamingly obvious. I certainly have more arguments about the nonexistance of God than I strictly should, given lack of evidence. So I have to acknowledge I'm not being as perfectly rational as I should be. To make that clear, I consider the rational position to be "we have no evidence for the genesis of the universe, beyond cosmology (big bang radiation and the such), revelation is not a proven way to achieve truth, nor is conviction or belief; on the contrary, evidence abounds that these techniques almost inevitably lead to falsehoods. Therefore, the default position is there is no god (like my default position is there is no Santa Bunny); any reasoning beyond that point (pro or con) is likely to be in error.
I apologize for the length of this point - it is the result of thinking "out loud", and it doesn't have a single, well defined and justified point. I just want to suggest that if you are arguing seriously about people, say, believing because it makes them happy, look to see how much evidence/empericism/logical arguments your argument consists of. The more you lean towards the latter, the more speculative your point, and the closer you are to the Georgetown Jesuits. Food for thought.