This song talks about faith, I think. People who don't believe in God tend to say first, "where was he?" where was he when someone I loved died, where was he when things went wrong, where was he when I was so lost... there are so many questions and so many ways in which people see faith as something incredibly real and physical in the sense that if God is alive then he should appear. It's not like that. Still, this sons applies to that rage of not knowing what is going to happen and knowing that God "wasn't there" supposedly.