Over time the surface will start to wear down. Imagine a perfectly rounded pencil lead wearing down and developing flat edges in the places where it's most used; it's just like this, only it takes a very long time.
If you use a matte screen protector to increase the friction it happens quite a bit faster, but on the screen glass you can generally use the same tip for a very long time.
At the extreme end you can wear away the surface to the point where the metal emitter in the tip is visible, and that's what Apple is referring to when they say that a damaged tip can scratch your screen. This can also happen if the tip is damaged by a fall, rubs against something very rough (like brick), etc.