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A lot of it is probably just laziness. I've not dealt with an PDF ebooks yet, but I deal with PDFs of scholarly journal articles all the time, and it seems the bulk of them are just scanned images of the printed pages. Of course a lot of them are older articles that the publishers probably didn't have an electronic copy of to make into a more e-reader friendly format and just had to scan the old journal.
I just print them out as I mark the hell out of them and find it easier to do on paper. Maybe some day when there's an A4 sized reader out with a touch screen that you can write on with a stylus just as easily and lag free as you can with a printout and a pin I'll give electronic versions of them another go.
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