If you don't mind my asking, what were some of those difficult questions? If you are comfortable in sharing them I would be interesting in knowing what they were, especially ones that were so difficult you lost your religion from them.
Short story:
I got to see a very dark world on an intimate personal level, and questioned how could god possibly exist in such a world.
Long story:
When I was 15, I fell in love with someone, who happened to be a guy, like me. His step-father was a very religious, bible-thumping, violent alcoholic, who made hating religious people easy. After spending many sleepless nights consoling my crying bf, who was hiding out in the basement trying to drown out the sounds of violence from upstairs, my first question was why is his step-father supposedly a better person for being so much into Christ, when he drinks so much, yells at my bf, and hits his wife? After dealing with the fear of our relationship being found out, and as a result me being ostracized at home, and my bf being kicked out of his house or simply beaten to death (he's in one of "those" states), my second question was why is the whole world telling us that we are committing a grave sin worthy of death, when all that happened was that we fell in love, something that's beyond our control and seemed beautiful to us?
The next thing that happened was that I was part of an online community that happened to include a lot of other kids my age, who used the privacy and anonymity of the internet to find other similar souls, share interests, and confide in them. Being extremely compassionate and fascinated by psychiatry/psychology at the time (very high IQ, and way more "grown up" than others my age), I got a chance to hear and console allot of guys and girls who were struggling with fear of and actual rejection from their parents because of their sexuality, various physical and sexual abuses from their parents, and who were just living in really shitty conditions that, being under 18, they couldn't do anything about. These were really horrible stories from people I ended up knowing very intimately, many of whom I ended up considering very close friends. On a few occasions there was eventually news from others that one of these "friends" committed suicide, or someone admitting, after being away for a few weeks, that they were in the hospital for attempting it. Eventually, after a nervous breakdown or two, it got to the point where I eventually got jaded, not wanting to listen to these stories anymore. Being immersed in all this, and being personally involved due to also recently finding out I'm not straight, affected me tremendously, leading me to nearly abandoning highschool, and landing me at a psychiatrist's with severe depression myself. In this particular dark part of my world, the third question that came up was why would god completely ignore these kids and their struggles, and just allow it to continue to happen? After all, these were not criminals, or bad people, they were just innocent kids who didn't do anything wrong, and had no control over their situations. There was no reason or purpose to their suffering. And that question eventually morphed into the last and final question, which was, how can god be so evil as to allow for a dark, extremely vast, yet unnoticed world like this to even exist?
From there it was a pretty easy step to simply realize that god most likely doesn't exist. If he does, at this point I think god would have to be the one to apologize profusely to me and my friends for
his sins, and even then I doubt I would forgive him. From all that I have learned since then, if god was, by some chance, real, I would be one of the first in line to wage war on him and try to bring him down for all the horrible injustice and suffering he has caused. Keep in mind, this isn't a "woe's me!" sort of thing. I wouldn't be demanding an apology to me personally, but on behalf of the many others he has wronged. But he's just a made up story, and it's much easier to think that there isn't anyone out there turning a blind eye to things, instead of knowing there's some horrible monster out there with the power to stop things, who chooses to simply watch.