Windows is far more riddled with malware and spyware than Linux distros, their users are far more ignorant than the Linux crowd, so having %ProgramFiles% default to a system directory is substantially worse and damaging than letting apt-get (that can't even be run without root privileges) default to /usr. Take a look at a list of predefined paths available on Windows [1]. It doesn't have anything even approximating ~/bin. At the very least they could've said - "here, use %UserProgramFiles% if need be", but they just don't care. And if you try and install into C:\Users\...\Program Files, you will quickly be mis-detected as malware or spyware. Unless you are Chrome, which you are probably not. So, yeah, Windows is really hopeless.
You keep mentioning ~/bin, but I don't think any major distro ships with such thing. So I don't really see how the situation is any better on Linux than it is on Windows. And then Windows has the Folder Virtualization trick.
> And if you try and install into C:\Users\...\Program Files, you will quickly be mis-detected as malware or spyware
So it's Windows's fault if you use crappy anti-virus applications? If you'd use similar applications on Linux wouldn't it equally flag ~/bin as malware too?
[1] http://msdn.microsoft.com/en-us/library/windows/desktop/bb76...