I really disagree that books are a perfected medium.
Novels often have to be broken in in order to open wide enough to comfortably read them, and well-used books fall apart (my poor physics textbook especially is barely hanging on). Print and paper quality can be enormously variable, it can be very difficult to re-find a meaningful passage, and many books don't have the features the author prizes whatsoever. It's also difficult to share notes on a work in a way that augments the original work.
That said, websites have many, many reading anti-patterns, our systems and tools lack ways to annotate, and even within formats that allow that, the ergonomics are quite bad. There's a variety of reasons the status quo it like this, but chief among them is probably money, "ownership," and copyright.
I finished my degree when digital textbooks were juuuuuust barely becoming a thing, but I distinctly remember limitations on how many words I was allowed to copy from a book, and that instantly turned me off ever using a textbook through a publisher's tools again.
More widely available, "open" books and tools would improve the situation, and you can get better accessibility through piracy, but without mainstream adoption and investment the situation will remain bad.
Sites like http://arxiv.org/ for papers have been a big leap forward for information availability, but there's still a lot of room for improvement for, ya know, reasons above.