The act of clicking on links and adding bookmarks, well, just doesn't feel the same as interacting with a physical book. I think the 3 dimensionality of the book adds intuition, cues, and a coherence that are lacking in the free for all of hyperlinks.

I also think an experienced reader can navigate more quickly (yes fraction of seconds) in a physical book than possible when you have to set bookmarks and use them in some drop down system.

I would love to see a human factors study comparing hyperlink eReader versus paper book.