To my knowledge, the reason behind this has to do with the fact that our planes have symetrical wings and require some angle of attack to generate lift. Hence on a flapped airplane by setting the elevator with a bit of down relative to the flaps when you neutralize the elevator the flap now is down a touch which creates some positive angle of attack on the wing while the airplane is still level relative to direction of flight. I beleive this is where the stabilizing affect comes from. I do know on several of my flapped planes, this trick has helped calm it down in level flight. However, I do beleive that what Ty says is also a factor.