It helps alert the user to how the data they are being shown is changing.
There are lots of non-skeuomorphic animations that could serve this purpose... cross-dissolves, flashes, slide-ins, etc. This just happens to be a reasonably nice one, that fits with the "this-is-a-book" metaphor of iBooks.
Even the name of iBooks is "skeuomorphic". It would be more accurately called "iMedium-to-long-static-documents-available-for-purchase" but that's a fucking awful title. Everybody has an idea of what a book is, so calling it iBooks means users know that there are book-ish-things contained within.
An app called iBooks where the next page trickled down like the title sequence from The Matrix would be tacky as hell and users would ask themselves why their "book thing" was doing this non-book thing.