The reason I've always heard (and sounds reasonable to me) is that the flags are painted the way a real flag would be flown on a pole.
Since the flag attaches to the pole on the side with the stars, as the plane flew it would be blown "backwards", like this:
Code:
-------*****I
-------*****I
------------I
------------I
I
I
I
<---- (wind)
Sorry for the amateur ascii art, but I hope this makes sense!