The wellspring for both the idea of the air force hitting civilian targets and the Rules of War set by the Geneva Accords dates back to the 19th century, in the American Civil War. As one of the first modern wars, it was the beginning of war going from a noble excercise of the elite and a means of negotiation to a horrible thing that was to be avoided.

The most famous example of why this happened is, of course, William Tecumseh Sherman. He is sometimes referred to by his first two initials, W and T, because his was a method of Total War. He realized that in order to win the war against the Confederacy, he had to do more than simply beat its army: he had to keep it from rising again. The only way to accomplish this was to cause as much pain for Southern civilians as possible; to bring the war to the people.

Therefore, he burned Atlanta. Therefore, he cut a swath 50 miles wide through Georgia wherein he destroyed everything from food supplies and railroads to trees and grass. Not only did this serve to break the Southerners' will to resist, it also kept them from resupplying their army. This is the premise behind the Air Force bombing civilians: not only must they defeat an opposing Air Force, but they must also win an economic war.

This is, of course, horrible, as made clear by such events as the Rape of Nanking and the bombing of Hiroshima and Nagasaki. Events like Sherman's March to the Sea led people to reconsider war as a horrible thing to be avoided at all costs, and also led them to attempt to prohibit the involvement of innocent civilians.

The reason that you see these conflicting views within the military, dr, with some people saying to leave the civilians alone and some people killing them en masse, is that both of these views are still widely held and come into conflict, even within organizations like NATO. It is simply far easier to bomb a faraway bus than to send soldiers to violate and kill women with bayonets. The result is the same but the public's aversion and the commander's guilt are far less.