Well, CP/M actually had a number of "user areas", the default one being USER 0. Some tools actually used that to simulate directories (AFAIR they kept the number to name mapping in a hidden file somewhere).
Once you have the basic concept of a filesystem, mapping names to chunks of data, I think directories are a natural extension. It's an aid to both the human and the computer.
It's only when you start having high capacity (5mb or so) fixed drives that directories are really needed.