Nomenclature aside, with "natural" scrolling you are moving the content while with the traditional scrolling you move the viewport. Imagine a scroll area like a window over a big canvas. In the traditional model, you move the window. When you scroll up, the window moves up and so the content moves down. In Apple's 'natural' model, the window is essentially fixed and what you move is the canvas beneath it. When you scroll up, the content goes up. I can kind of understand why they call it 'natural' — the movement of the content directly follows the user input rather then moving in the opposite direction.
Why is the traditional method more popular? I believe it has to do solely with historic reasons. It more closely mirrors how scroll views are usually programmed, so it was easier for programmers to implement when scroll views were first invented. In the end, it doesn't really matter. I am not aware of any benefits of this or other scrolling methods. It takes less then few hours for your brain to 'flip' the expectations this or other way. When using trackpads, I certainly prefer the 'natural' method, because it offers the same experience as a touchscreen.
