I Timothy 2:1-2 tells us to pray for everyone, and to be certain to pray for those in leadership (kings in that day, but president for us). That also, in my opinion, means praying for the civilian leaders of our military. While that does include the President of the United States, it also means the Secretary of Defense and of the Navy (which includes Marines), Air Force, and Army, and since we include the Coast Guard in Military Prayer Week, include the Transporation Secretary as well.
As is the case for anyone working for the government, these men (and women in some cases) put into place the policies that affect military personnel the world over, regardless of faith. In some cases, they can indeed create or change policies affecting faith, or the exercise thereof. On the immediate horizon is Don't Ask Don't Tell (DADT), as an example. It is not my desire to go on a political stump speech, but it is important to humbly and honestly pray to our Father for our civilian leadership.
Won't you join me?
Dear Heavenly Father,
I pray for the Secretaries of the Navy, Army, Air Force, and Transportation today as well as the Secretary of Defense and the President and Vice President of the United States. May they establish policies that allow the Christians in uniform to continue celebrating their faith freely. May they never place the military in harms way without a cause.
In Christ's Name,