Are books ugly?
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.
Digital books can be more than simply text on a screen as well; I noticed in a recent Amazon title that passages which were frequently highlighted by other users were set differently (I think it was a highlight as well; I can't remember the title I saw it in). Never mind the privacy concerns; it's the morphing of a medium.
On the other hand, applying the skeuomorphs of such a thing cheapens it. It's a mask, trying to hide its nature. For me, it's almost an uncanny valley feel. And I think the best design is that which unleashes full intuitiveness: if I had never seen a book, why would I expect this animation to be there when reading an e-book? It's superfluous to the nature of the media.
Even the page turning itself is superfluous to the media. Its purpose is to add pauses to the interaction. You lose part of that experience when there is no longer a physical page.