Mac OS X, I think, has done a decent job of structuring the file system to be more user friendly despite the -nix background.
Modern use cases typically revolve around either installation and use of specific applications, often with dozens or hundreds of files needed, and data storage. In Windows/Mac, applications (for the most part) are installed into their own individual application folder and a GUI (as opposed to the PATH) is used to provide easy access to the application. This makes it easy to 1) know where to put a program you're installing, 2) know how to locate a program after install, and 3) keeps all the application components in a single place for easy move or removal.
In my somewhat limited experience with Linux, I find that the complicated nature of the file system makes package management systems necessary to simply keep track of where all the files are: executable in /usr/local/share/bin, configuration files in /etc, libraries in /usr/lib, and I'm not sure where non-binary resources of an application get stored.
I once installed my favorite browser (Opera) in Ubuntu. It didn't make a desktop or Applcation menu icon for some reason, so I figured I'd just go make a icon to point to it. It took quite a while to just figure out where the executable was at.
This could very well be one of the reasons that many people find Linux on the desktop difficult to use. They don't understand where anything goes.
I hope that one day one Linux distribution will at least step up and consider restructuring the file system to be more friendly and straight forward and to take advantage of the availability of long file names.