Civilian rule is a fundamental principle of American democracy. It is intended to protect the people from the alternative, which would be military rule. As can be seen in countries where the governments are headed by uniformed generals or "juntas," military rule is usually closely associated with dictatorship. The top military officers in America have always been willing to accept the principle of civilian rule, even though the president might have no military experience at all. As president he has the power to call on military experts for advice, and his decisions are usually based on such military advice, along with advice from experts in other aspects of world affairs.
The celebrated confrontation between President Truman and General MacArthur during the Korean War was regarded as a threat to civilian rule. MacArthur was an outstanding military expert and leader as well as a war hero, and Truman's military experience was limited to service as a junior officer during World War I. But MacArthur ended up getting summarily fired because he balked at obeying orders from the civilian commander-in-chief.
Civilian rule is not only a good thing, but it is of the utmost importance to preserving our democracy.