There's a lot of theological debate among many religions about the "all powerful" aspect - it's been troubling throughout history, but it particularly reared its head in post-Holocaust times. Many religious theologians have shifted, saying that God is all-loving and all-knowing, but not all-powerful. They say that God gave up some power when humans were created, and it is the job of humans to complete the work.
So, when people say "Where is God amid all these bad things?", many answer that God could not intervene in the Holocaust or the Sudan strife or Vietnam or the school shootings, 9/11 or the AIDS epidemic. Instead, God was in the hands and minds of the rescuers of Jews, the intrepid spirit of those who walked hundreds of miles and endured African refugee camps, the spirit of reconciliation with Vietnam now, the brave teachers who shielded children in Newtown, the first responders after 9/11, and the scientists and doctors who work with AIDS patients.
Perhaps, by that argument, God IS answering your son's prayers by giving him the strength to talk to you, to stand up against bullies, to be kind to others so no one else has to feel this way. Perhaps God wants your son to start (or help) an organization in school to bring light to the bullying problem. There's a common expression that we have to "pray with our feet" - that we can't just pray in a vacuum and leave the work to God, but we have to pray for strength and inspiration and then get off our butts and do the work.
My son told me he was an atheist around the same age. I mentioned it to my rabbi, who said, "Don't worry. They ALL are at this age! Focus on what he does and how he acts, and not on what he believes."
So I would say to my son that there are plenty of people who profess a belief in God and a love for God, and then turn around and do cruel, callous, discriminatory things that give God pain. It's like people who make a big deal about the Pledge of Allegiance but then are not patriotic in their actions. It doesn't matter what people say - it matters what they DO! So, he's 17, he's becoming an adult, and the world's realities are far more clear to him than when he was 12 or 8 or 4. So, he needs to come into his own adult reality and decide that he has a job on this earth, which is to make his own corner of the world a little better and not be a victim, expecting everyone else to do it for him.
I think, if you are a member of a church, you might benefit from talking to your clergy person and perhaps having your son do so as well.