This is another answer to Where was God that I received in an email.

If God really cares, why did He let this happen and where was He?
If you look carefully, you'll see that God was awake and was most certainly there. God was on United Airlines Flight 93 giving courage to Thomas Burnett who, after hearing the news of the World Trade Center, told his wife via phone that they had been hijacked and that, "there's three of us who are going to do something about it." Shortly thereafter, the plane exploded into the Pennsylvania countryside. God was with Billy Wik who worked near the top of Tower Two. Mr. Wik called his wife to say, "I'm gonna get out, but I have to get my people out" and has not been heard from since. God was with the multitudes who evacuated the towers before the buildings roared to the ground. God was with the two police officers who were in the lobby when it collapsed on top of them and somehow survived in an air pocket beneath the rubble. God was with the five firefighters who were rescued on Thursday morning after they had become trapped while searching for others.
And God was there too, with the thousands who died too soon at the Pentagon, in Manhattan, and in Pennsylvania. God was there-crying as His children struck down their own brothers and sisters.
And now God is with the multitudes lining up to give blood. God is with the volunteers and rescue workers who keep clawing away at the rubble through the choking smoke and ash to find, beyond hope, one person who is still alive. God is with Billy Wik's wife and the three children he left behind. God is with Ms. Burnett and the families of the three others who paid the ultimate price to save so many lives. God is with the myriad who mourn the unspeakable, excruciating loss they must now personally endure as a result of this evil act.
And God is here, now, with you-crying with you and encouraging you to go forward in hope and faith; knowing that He will indeed wipe every tear away; that He will make every wrong right; that He will give you the strength to live another day so you can show to the world that God is indeed there.
-Karl Leuthauser