It's not so much that Rattrap is a coward... he just doesn't want to die. He's seen enough battles to know the score, so he's not afraid to tell his commanding officer to shove it if he's not fond of the odds. He prefers to sneak around unseen, in gutters or trenches or trash barges or what have you—whatever keeps him out of harm's way. He shouldn't be so worried. When he does encounter conflict, he deals with it masterfully with the arsenal of guns and bombs he keeps on himself at all times. He feels naked without them.