Go back 40/50 years, and most people then thought of directories as an index (see telephone directory), and folders were thing that contained/were files within a filing cabinet.
I still have a hard time calling them folders, it gives me a little eye twitch to say "folder", though I know the icon is a folder, and it makes it easier for the average person to grok.
That always bothered me, from the start.
"Apple is more intuitive" oh really?