The disciples wondered the same thing after Jesus was crucified. The Jews who went through the Holocaust wondered it too, along with everybody on earth who has suffered some great loss. I don't have any answers, except to look back on how God has worked in my own life, to believe the spiritual is more important than the temporal, and to think we don't escape the consequences of our (or other's) actions. But having said that, I have also seen people asking where God was when they previously didn't even believe in God. I always wonder why people who don't believe in him blame him for everything that happens.