In defense of organized religion, I know people who have had the opposite experience; i.e., whose teachers, pastors, and priests were very encouraging of questions and did their best to answer them. I have heard that the Catholic Church in particular is much more welcoming of this (or was for one person, anyway) than I had expected.
I wish those people were more forthcoming. I am deeply and devoutly religious, but I don't blame many for their reactions to religion given its common course. I was always taught to ask questions. My teachers, parents, and other role models were generally welcoming and did not seem afraid of inquisition (in fact, they would invite it, and invite us to explore other religions -- the opposite occurs in most Christian denominations), and I think that played a big role in my continuance in the faith.
There is a deep, endless reality to pure religion, found in many sects. Most, however, follow their religion because it's part of their tradition, and it's something that makes them comfortable. They have a very superficial understanding of its components and mainly practice (to the extent that they do practice) to help themselves feel better. Of course, when challenged, they take the intellectually lazy out of belittling and discrediting the source instead of ever considering their questions on a philosophical level.
That is not pure religion. Pure religion is a rigorous, demanding, constant program of self-improvement, discipline, learning, and love. It can be found in many sects to the degree that its practitioners embrace and internalize the principles espoused. Pure religionists love inquisition and they love learning. They are also generally more intellectually active and less likely to tout religion as a badge when pursuing political office (not that that happens very often either), etc.
To you atheists, we know you've had bad experiences, and we know that there are a lot of people out there trying to embarrass religionists, but please remember that there is a non-vocal minority, much smaller than the general religious population but still not insignificant, for whom religion is deep and serious, and not a matter of silencing curiosity to make way for comfortable lies about ourselves.
I found a book at my local library that I really loved. "The Faith of a Scientist" by Henry Eyring [1], a brilliant chemist and devout Mormon who has a beautiful, refreshingly rational take on religion. The chapters are succinct and cover specific scientific principles that often receive a lot of undeserved friction from religious people - the age of the earth, evolution, etc. There doesn't have to be a discrepancy between intellectual curiosity and religion. I recommend it to all of my friends who are religious but find the general attitude of those within their faith intellectually unsatisfying.
In defense of organized religion, I know people who have had the opposite experience; i.e., whose teachers, pastors, and priests were very encouraging of questions and did their best to answer them. I have heard that the Catholic Church in particular is much more welcoming of this (or was for one person, anyway) than I had expected.