This is the opening to the first chapter in my book. Comments/corrections/suggestions are welcome.
Moshe sat in the waiting room, a little nervous, a little hopeful. In many ways, he was a typical yeshiva bochur. He had spent a couple of years leaning full-time after high school and was now learning part of the day and in college in the evenings. He dressed the same as the other bochrim in his yeshiva, listened to the same frum music that they did, went to the same events, and kept all of the mitzvos. Yet, in one important way, Moshe was different.
His fellow students had no problems with their emunah, but Moshe was plagued by questions. He wanted to know the reasons for mitzvos. To understand how many things accepted by the community, like segulos, worked. To square strange statements about the world in tanach and the gemara with how he knew the world to work. As a teenager, the principal of his high school had called Moshe into his office one day and told him that, while Yiddishkeit allowed one to ask questions, even encouraged it, he should stop asking his questions in class. These questions didn't occur to the other bochurim, and why should their emunah chas v'sholom be weakened by Moishe's questions?
Moshe was a good kid, and he did as the principal asked, but the questions didn't go away. If anything, the more he learned about the world, the stronger they became. Moshe sought out and read kiruv books that promised to answer questions of emunah and prove the Yiddishkeit was correct. They were disappointing. Every now and then Moshe would come across something that seemed convincing, that seemed like it could be the idea on which he could rebuild his faith. Within a week or two, as he thought about the exciting new concept, he would sadly realize it was full of holes. It relied on logical errors, or didn't match up with real-world experiences, or contradicted other things Moshe had learned in yeshiva.
Moishe's interest in his religion blossomed into an interest in the history of Judaism, in comparative religion, in philosophy and mythology and biblical scholarship. The more he read, the less tenable yiddishkeit seemed, until one day Moshe realized that he couldn't avoid the obvious conclusion. Judaism wasn't true, and there probably wasn't a God. The realization upset him, and he felt a deep sense of loss, but there it was. Still, he thought to himself, maybe this is all just the yetzer hara, trying to convince me not to keep the mitzvos. He continued to keep the mitvos as meticulously as he always had.
A year went by. Keeping the mitzvos while not believing in Judaism in order to make sure it wasn't the yetzer hara planting thoughts in his head was starting to feel faintly ridiculous. It would soon be time for Moshe to start dating, but how could he in good conscience go out with Bais Yaakov girls when he didn't believe? In a last-ditch effort to regain his emunah, he had a friend put him in touch with a kiruv worker. The rabbi came highly recommended, and Moshe met with him a few times to discuss his issues with Yidishkeit. The rabbi was friendly and seemed genuinely concerned about Moishe, but like the kiruv books, his answers were disappointing. A week ago the rabbi had called Moshe with exciting news. He had gotten Moshe an appointment with a big rav, a real talmid chocham who would be able to answer Moishe's questions, help him see that Torah and Yiddishkeit were the emes and regain his emunah.
At last Moshe was ushered into the rav's presence. The rav asked Moshe why he had come, and Moshe explained that he had questions of emunah that bothered him, and gave a few examples. The rav listened, then gave Moshe a bracha that his emunah shelaima should return.
"I was hoping that you could answer some of my questions." Moshe said.
The rav quoted the Brisker Rav and said "I answer questions not excuses." He explained, "You have decided to be porek ol, since you did not control your yetzer haras, and you found an excuse that you had 'questions', and I don't answer excuses!"
The rav gave Moshe another beracha that he would merit teshuva shelema, and Moshe was ushered back to the waiting room.
The above is a composite story, combining my experiences and those I have read or been told by others who have had the misfortune to be frum and skeptical. Elements of it would be recognized by anyone who has been in yeshiva and questioned ikkarei emunah. I thought about religion while none of my fellow students did, I was told by my high school principal to stop asking questions, I wanted to understand how Judaism works and how religious ideas square with the world I experience, and I found that the more I learned about the world, about history, theology, philosophy, and science, the less tenable Yiddishkeit seemed. I have read accounts by people who continued to keep the mitzvos for years after losing their faith because they were worried that their questions might be the yetzer hara trying to fool them into giving up the mitzvos. Many people have related the sadness and sense of loss they felt when they realized that Judaism wasn't true and there probably wasn't a God. And many people have talked about how maddening it was after years of searching for answers to have their sincere questions dismissed as excuses to be porek ol. The conversation between Moshe and the rav is lifted nearly verbatim from an account an encounter between three questioning bochurim and Rav Chaim Kanievsky.
Many frum people believe that Judaism is obviously correct. After all, at the midrash tells us that Avraham Avinu figured out that Hashem was the master of the Universe when he was only three years old! It's obvious even to a child that Hashem runs the world. Yet if it's so obvious, how could anyone go off the derech? How could anyone disbelieve when the truth is staring him in the face? Chazal answer, "lo uvdo avodas kochavim ela l'hatir lahem arayos," "[people] don't worship idols except to permit to themselves sexual licentiousness." The person wants to do aveiros, but he can't because he knows Hashem will punish him. So he comes up with "questions" that allow him to convince himself that Hashem won't punish him after all, and he can do whatever he wants.
The thesis of this book is that those who reject the tenets of Orthodox Judaism are not hedonistic cretins looking for excuses to throw off the ol hatorah and wallow in their taivos. That it is not obvious that God exists and that Judaism is true. That there are serious questions that undermine Orthodoxy, Judaism, and belief in God. That it is reasonable to doubt Judaism's tenets and act on those doubts. That doing so is more reasonable than clinging to the belief that the tenets of Orthodox Judaism are obviously true.
 See http://baalhabos.blogspot.com/2006/08/orthoprax-at-home.html for one example
 Bruer, P. (10/21/2010). Al teirutzim ani lo onah teshuvos. HaShavua Retrieved from: http://shiltonhasechel.blogspot.com/2010/11/excuses-not-questions.html 6/5/16
 Sepher Ha-Yashar 9:13-19 This is a polemic against idolatry rather than an argument for God's existence or the truth of Judaism.
 Sanhedrin 63b