Ennnnh... I've got to disagree.Attacks against military targets are by default more moral than attacks against civilians.
If we're talking about tactical or strategic targets in an actual war, then sure: it's reasonable to attack your enemy's ability to fight.
However, if your objective isn't your enemy's war-fighting ability but instead your aim is to spread fear in the citizenry, then I don't think the fact that the target is military excuses the action.
In the case of the Weather Underground placing a bomb in a Pentagon bathroom, I don't think their attack could reasonably be thought to have anything to do with limiting the US ability to wage war aganist either the Viet Cong or the Weather Underground itself.