Sorry, but people's comprehension problems are much more basic than that. The very idea of a hierarchical filing system where things can be put at any level hits a mental block. This is well before any detailed discussion of how any particular thing should be organized.
The underlying problem users have with software - as illustrated by the hierarchical file system model - is being required to make decisions than they are comfortable with. If you as an iPhone user simply want to edit and store a text file, you're not going to want to have to know the stories behind emacs vs. vim, the "everything is a file" ethos of Plan 9, or the sordid history of Hans Reiser.
Apple (and other minimalist UX designers) have the right idea here: remove all unnecessary choices and questions so that the user can solve their basic need. This is minimum viable product. This is Basecamp vs. MS Project. Add extra features (i.e. extra decisions to confront the user with) if necessary, but only if they prove themselves.
Non-technical users don't "get" the directory tree because it is a leaky abstraction that fails to consistently deliver on the assurances offered to users. It helps when deterministically planning a Unix filesystem but over time the system destabilizes due to inevitable mismatches between the expectations of OS maintainers, package authors, and end users.
- Underinformed users make best-guess choices (that contradict the intentions of the system designers) as to where to put new files
- Software authors publish conflicting install guides e.g. "sudo make install" vs. "extract to ~/bin/ and add it to your path"
- Symlinks - which are fabulously useful by the way - undermine the promise of a canonical location for each file.