When I started using Lion, the first thing I did was turn off ‘Natural Scrolling’. A week ago, I decided to try natural scrolling again. After using it for a few days, I started getting used to it, and a week later, I actually find it more natural.
The way scrolling worked in the past, you were manipulating the scroll bar, which acted as a window into your document, showing the portion of your document that’s visible in the window. Therefore, when the scroll indicator is at the top you see the beginning of the document. When you drag it down to the bottom, you see the end of the document.
With natural scrolling, you’re manipulating the document content rather than the scroll bar. This is the same way scrolling works in iOS. Since Lion de-emphasizes the scroll bar, this makes more sense. I still prefer to show the scrollbar as an indication of the document size, however.