Overall agree with the article: use individual apps that do well what they're designed to do, and use the file system to organize your stuff. Unfortunately, a tremendous number of users cannot make heads or tales out of the file system.

I believe the chief causes of the confusion are (1) different apps save newly created/edited files to different places (2) many users are clueless about navigating the file system within the Save As dialog (3) many users rely on an app's Recent list (4) many users don't know how to search their own file systems.

(1) Some apps always want to Save As to the Documents folder. Some always want to Save As to wherever you finished off your previous Save As. Some always want to Save As to the folder of the file you most recently opened in that app. Etc. No one can remember each app's convention.

(2) People don't realize they can navigate within Save As to someplace other than wherever the app feels like plopping the file by default at that moment. True even when shown over and over and over how to do this.

(3) Once you move a file, its entry in an app's Recent listing is probably borked. This sends people who rely on Recent for finding and opening files into a panic.

(4) They don't know how to click on the desktop and hit cmd-F or to click on Start->Find. And once they do, the Find window looks nothing like Google or a web browser. They don't understand what the various search criteria are or how to enter them. They don't know how to read the results.