The thing iPhoneOS is most intent on eliminating are deep trees of files. It does this by training the user to think of their files/content as being managed by an individual app that's responsible for manipulating it. This creates a single top-level "folder" for the user to use as a mental key to remember how to get at something.
Contrast that much shorter path to content to the standard desktop model of having a folder in your home folder, perhaps, to store documents. The ability to make sub-folders, sub-sub-folders, etc. and have all the contents of those folders utterly disconnected from the applications you use to manipulate and create that content. It makes sense to those of us who grew up/invented it, but for people just looking to use a computer as a tool in their non-computer-driven life suffer under the cognitive load of the foreign metaphors.
In my experience, people "get" that individual files represent their content. They do not "get" folder hierarchies, though, and find themselves easily lost within them. I think many non-experts consider an app as a destination and not as a program to run. It makes more sense to them to think of "going" to the app and then finding their content there than it does to "run" an app and then later point it to their content.