It’s actually white on black, or rather green or amber on black, that is the traditional way. I’ve used them all. 🙂
I believe that the use of black on white started in word processors, because it’s a lot easier on your eyes when you alternate between looking at the screen and looking at source material printed on paper.
Also, the contrast between the screen background and the surrounding lighting should be small, so a white background works best with the well lit room most people use computers in most of the time. If you are programming in the darkness a black background would give less contrast, but then it’s more a question of why you don’t have proper lighting in your room…
There are of course personal preferences than can affect your choise of color setting, and your eyesight (or lack thereof) might also make one setting better than the other.