For instance, consider these facts: (a) Reading is a major part of my job; (b) I annotate quite heavily the books I read for work; (c) I buy a lot of those books from Amazon in Kindle format. A while back I left my Kindle on an airplane, and the airline couldn’t retrieve it; but when I bought a replacement I downloaded all the books I had read and there my annotations were, unchanged. In fact, I didn’t even have to buy a replacement: I could have used the Kindle app for my Mac, or for the iPhone or iPad, or I could have read the books online, and in any of those environments my annotations would be present and identical. (On the web I can even copy and paste the passages I have highlighted and my own notes.)
Jacobs makes a very important point that ebooks are often far better tools for daily use. When Apple introduced Multi-touch books in iBooks 2, they made a big point about the ease of fast navigation in the textbook - something that is crushingly awful on a hardware Kindle.
At the same time, iBooks doesn't have a "back" button so navigating around a book via hyperlinks is fraught with the danger of losing your place (Clarification: this is true for multi-touch books but not for ePub books).