The President, a civilian elected principally by civilians, is Commander in Chief of the Armed Forces. That creates a protection from a military leader who could be tempted to assume dictatorial powers over a nation as frequently happens in other parts of the world. The Founders were aware of this from European History but more profoundly from classical history in the dissolution of the Roman Republic by victorious generals who became emperors.
We should see some of this in the movie "Lincoln" because that President was heavily engaged and involved in managing that war to put down rebellion, at least until he found the generals he could trust in Grant, Sherman, and Sheridan. Yet he still frequently consulted with them and engaged in the decisions as to how to proceed and ultimately bring more freedom, civil rights, and peace in the place of rebellion.
It appears to me that the former community organizer and law school instructor is in charge, not the hero of the surges in Iraq and Afghanistan. This gives me much more comfort about civilian control over the military than what we saw with the last President.
Petraeus's tragic and human fall from grace, especially on one of those "family value" issues so important to the right, should help deflate a little of the deference to military heroes who work for us civilians. This is an important correction to the war-emphasis of the last President along with the fact that our current President has extracted us from one war we never should have been in and working on getting us out of the other more necessary war that should have ended years ago.
I remember watching a report on CNN about senate hearing on the war. I am pretty sure it it was 2002-03 since I had young twins to nurse all the time, and so watching CNN was something I did. One reporter asked then President Bush something about Iraq. He seemed almost proud not to know many details. Part of what stuck out to me was that he said he slept well at night because the military had people who understood war better than he did.
At the time I had already decided that there were a number of deeply troubling thing about "Junior," but I was very uncomfortable with a president who outsourced his worrying. If nothing else, no one can say Obama outsources his worrying.