Who gave Cheney the authority?

Where does the VPOTUS fit in the military chain of command? According to the latest report from the 9/11 commission Cheney gave the order to shoot down commercial planes on 9/11. Does he have this authority? Even if the President told him to? As far as I know the VPOTUS' only job is to be the presiding officer of the U.S. Senate and break ties in the Senate. I don't believe that he has any authority to issue orders to shoot down planes. The Washington post has some good reporting on this issue. There is a reason the POTUS is the commander in chief is the he issues the ultimate orders. If we start having the VPOTUS or others saying that the POTUS told them to issue orders with no way of verifying those orders then who is really in control?

BTW POTUS = President of the United States.