It is all in the physics of the fligh path of the bullet.
Try this (or picture this), you take a fly rod attach a small weight to the end of a line attached to the end of the fly rod. Hold the rod horizontal. You will notice the tip is lower than the rod shaft. This almost simulates the path of the bullet. As you already know, there is an arc to the flight path of the bullet. Note where the wieght is position with respect to the ground.
Next start to raise the tip of the rod up. As it starts going up the arc or rod flex increases which would indicate that shooting at a target above your feet would cause you to shoot under your intended target ( the reference on the ground moves towards you). The more upward angle the more you will miss beneath the target.
The opposite will hold true for a target below your feet. You will have less arc therefore you shoot over the target. The steeper the angle the more you will shoot over the intended target.
This is more prevelant with blackpowder than with modern firearms, but the same principle applies. This also holds true for bow and arrow.
The next time you get a chance, climb a tree stand, shoot off the roof of a building, etc, at paper targets. You will see the difference.