In iOS, the touch interface is meant to mimic real world touch responses.
If you tear a page from a novel, put it on the table, then "flick up", the paper itself travels upwards, but if your relative eye position remains stationary, then the content focus "travels downwards" towards the bottom of the page.
Still not convinced? Take an iPad-shaped piece of cardboard with the "screen" cut out of the middle, hover it over the page, and use your finger to move the text up/down/left/right inside the 'screen area'. The movements will map directly to how a Kindle or iBooks page would on an iOS device.
So, to me, I wouldn't say that the scrolling IS inverted, it's just "pretending" that the digital content within an iOS device is real, and that you are really touching that content. Therein lies the magic – Apple is optimizing for the technology to disappear into the background, and for non-technologists to have a lower bar to entry by making their real-world touch skills and experience as transferrable as possible.