For one I think the example doesn't really fit, as Linux binaries are much closer to modules than they are to plain functions, as each of those binaries has numerous command line flags to change it's behavior quite radically. Functions as you encounter in a programming language are much simpler and more focused.

The other issue is that the approach is extremely inflexible, if you want to replace /usr/bin/program with a new version, everybody on the system is forced to use the new version, even if the new version might break stuff. Traditional `/usr/bin` doesn't provide a solution for this. You can of course work around that by using `/opt` or installing things in your home directory, but at that point you are just using the file system as namespace.