The problem is that the alternative is reading on your computer or reader - which sucks (for many) compared with a real book. For me I remember things more clearly when I read them in physical books because the information exists in a "space" - I remember reading something, pick up the book and flip there. I can recall things by remembering what was around them in the book. The tactile-ness works for my brain.
I totally agree they aren't worth destroying trees for (I only buy paper books for topics that are more age-resistant) but I get why people still buy them.
You put into words something I've experienced throughout my life--a sort of "spatial topical memory"--and it's refreshing to see others often do the same.
I like digital reference material for the advantages they possess (ease of searching, bookmarking, etc.) but dislike them for the same reasons you illustrate and others, such as thumbing through. It's strange how tactile feedback can become so important. It's also one of the reasons I wish publishers would do something like what Pragmatic Press does more often: Offer both the physical and digital versions of books (although if you're buying both, I'd rather the digital copy be a bit less expensive).
Since there are advantages to both, I'm reluctant to say one format is better than the other, but each is good at something the other isn't. Whenever I've read reference materials in a digital format, I find I suffer from a similar problem to yours: Recalling things in proximity becomes jumbled with other reference materials and works. There's definitely something to be said for a physical medium even if it's not near-instantly searchable and required physical bookmarks.
Then again, I can't plug headphones into a dead tree and read it in complete darkness. (Setting it on fire doesn't count.)
I totally agree they aren't worth destroying trees for (I only buy paper books for topics that are more age-resistant) but I get why people still buy them.