Ewe - windows media player.
just a horrible example for any subject.
I don't mean throw everything into one flat directory, although it shouldn't matter. But let's say someone is a book collector, publisher, reviewer, or average user with some distinct sets of readable material, say text books they bought online, technical manuals for work, children's books, wife's digital magazines - user may want to keep it in a structure like this (example):
/ebooks/textbooks
/ebooks/work
/ebooks/magazines
This is easy for a backup services to traverse, if structure doesn't change offten (with each book title rename).
Easy for windows index service to keep tabs on file location. (Google desktop looks like is no more - discontinued).
If you need to send a coworker a bunch of work related pdf's - you may need to go back to the file system, zip up a bunch and emai them over.
Easy for a user to replicate a library on another computer.
But then, author/title file structure "works" too. There are ways around it. I personally keep the original files separate from those procesed by calibre. One day there maybe other apps that I will need to use, on different OS's. Maybe one day all of the books I store locally will go into the cloud.