I believe it's main sore point for me is the underlying assumption that the society of faith knows best and that suffering happens for the greater good. As B mentioned in book club "I'm a happy person, am I beyond salvation?" The idea that someone must be utterly broken before god can mould them to his purpose is uncomfortable to begin with before you add the question of who is involved in the remaking.
Honestly, I just can't separate the politics from it. I constantly look for some way to reconcile the faith to the politics, but it never addressed by religious leaders (at least the ones I have found). I don't the solution.
A more personal fear I have alluded to with the title. The book fool is rarely from my mind. With authority easily questioned, I often wondered whether I'm reading the right books or not. Perhaps Wilde was right to say there are only well or poorly written books.
All this from a cheap sci-fi book.