It's a question of jargon. What does the layperson think of when they hear "directory", a telephone directory? Whereas if you call them "folders" or even better, as on the Amiga, "drawers", then it all becomes very obvious.
Not really - it is not very intuitive that you put folders into folders and have all your documents in one big folder containing all your other folders. And you don't have drawers containing other drawers either, in the real world.
But apart from bad metaphors, I thing non-geeks have a problem with organizing things in arbitrary deep hierarchies. You don't really do that a lot outside of computing.
When I started out using computers, an adult explained it to me using a shelf as a metaphor: The drive is a shelf. You can have multiple shelves. Shelves have compartments, which contain things. Some of those things can contain other things, like boxes or folders. Made the nesting rather obvious to me.
I should probaly have said recursive hierarchies is not intuitive for everyone. Everyone can understand shelves in drawers, boxes on shelves and so on. What is confusing to many is folders inside folders or drawers inside drawers arbitrarily deep.
The problem is not directory, it's the hierarchy.
The first time I have this described was a looong time ago when reading Alan Cooper's "About Face".
I guess this is not news to anyone who is interested in UI and UX.
Obvious? Then you must be in favour of Apple's move to 'at most one level of hierarchy'. Or do you find the concept of drawers inside drawers inside drawers intuitive?
Not to comment on how it works in a UI, but my chest of drawers at home does indeed have two levels, there is a smaller drawer (for socks) inside the main top drawer.
Call 'em "boxes" or "bags" for all I care - the point is the geek word "directory" isn't suitable for non-technical people, I think everyone understand the concept of "putting things in things" because they do it all the time in the real world.
I haven't seen the word "directory" widely used amongst laymen since the move from Windows 3.x to Windows 95, where if my memory serves me (I was 9 at the time) Microsoft made the change to "folder" themselves.