Most carry calibers of handgun rounds will go through a car door with enough force to injure or kill someone on the other side.
http://www.theboxotruth.com/docs/buickot3.htm
Is it a preferred shot? Absolutely not. Is it likely to work? It very well could.
From my own experience with neighborhood punks with BB guns, car doors are for decoration and to keep the rain out. A friggin BB gun. Gonna type it slowly again
B . B . G . U. N., penetrated my car door (at least the outer metal skin).
In the event the window is already broken and perp standing there, getting a pistol up near my face and in the perps reach may not be advisable. In which case, a shot through the door into his legs / crotch area may be my best option. The shooter may be burned, and deaf afterwards but that's no worse than accidentally shooting my own left arm or losing the gun to the perp.
Really though, lock your damn doors when you drive. That'll buy time and force them to break a window. (And, in WI, now counts as forcible entry for the new "castle doctrine" law so you'll be civilly immune.) Stay out of riot zones where the first attack will be done with a brick.