I think it is just a muscle memory issue. Everyone seems to have gotten used to scrolling on the iPad without complaint (and it feels pretty intuitive). The new default is the same scrolling. It just feels wrong because we learned it the other way. If the original design of scrolling mice was in the opposite direction we wouldn't be having the conversation today.
I believe it goes deeper than that, Terry. An iPad is a touch based device ... you are manipulating the virtual thing itself. With a scroller and a scrollbar, you are manipulating the position of the view, not the virtual thing itself.
Imagine a piece of paper on your desk and a window that you can see it through which is smaller than the piece of paper. When you want to view the bottom of the page, you don't slide the paper up, you move the window down. That's what the scrollbar-scroller control is modeled on, not the touch-based operation of moving a piece of paper with no frame across your view. It's a matter of perception and frame of reference.
And that's the last I'll say about it as it really is a pretty unimportant issue ... After all, Apple recognizes that what they chose as a default might not be everyone's preference and provided an option to make it work the right way.
]'-)
Just like some people like Nikon, some like Canon ... some like Sony NEX, some like Panasonic Lumix, and some like some other cameras simply because they work the way a particular person wants, to bring it back to photographic things.