Today's society (at least in the west) is heavily influenced by Enlightenment ideals, and the ideas of "gentlemanly" war. This includes the killing of civilians and, to a greater degree, applying moralism to war.

In feudal societies like England and Japan, as you listed, would have had very little if any remorse about taking an enemy's land, or killing large numbers of soldiers in a war. In fact, both societies did this frequently, with Oda Nobunaga's battles for Japan. England, on the other hand, viewed feudalism as necessary to repel raiders and (for a time) vikings, and thus nobles and kings with armies were viewed by the average populace as "in the right" to kill. But during things like the invasions of Normandy (the Medieval invasions of Normandy), proto-nationalist tensions tended to make France and England's citizens hate each other, despite having only a loose culture-language bond to constitute an early nation-state.

Rome was a different entity, as it was not feudalistic, and relied on a system of citizenship and assimilated peoples into the empire via a sort of "second-class-citizen" basis. It was essentially you were a Roman or you weren't, and Romans typically did not feel bad about killing non-Romans. This tied into cultural ties and religion, as with Jerusalem and Egypt. Tax rates were also significantly higher in puppeted, non-Roman provinces (this is one of the reasons for Rome's fall, but it is besides the point).