That is until they need to scavenge and mess around the file system because of a virus, failed uninstall, missing DLL or something. Then they really care.
If that's the problem, what's the better approach to solving it: cleaning up the file system organization, or making it so that those things don't happen and make people mess around with the file system in the first place (e.g. by introducing a declarative isolated application model such as AppX in Windows 8)?