You said it yourself, free beats everything else. For the vast majority of people the OS is free, they either buy a Mac (OSX already installed) or a Windows PC with Windows already installed. So installing Linux is actually not free (it requires extra work).
I would actually not be surprised if the market share of Linux exceeds the market share of Windows where Windows was installed by the user (let's exclude corporate environments because the discussion is much more complicated)
No, the point is just because something became popular doesn't mean it was because it was a high quality product technically or in UI. The early iPods sucked in usability (controversial!) And functionality, but became popular anyway. I had to support them, they, coupled with iTunes, we're horrible. People just learn to use them and eventually one quirky way of doing things becomes 'the norm.'
The 'Linux Desktop' is just as solid as Windows... depending on what you do with it. Just as Windows could be horrible compared to Linux... depending on what you're doing with it
Network effect, relative difficulty of switching an OS and familiarity . It even heavily effects OSX, which has the marketshare it has due to its platform integration, more than anything.
It is not a fair competition.
Users will shop around for web browsers and everything else but settle for Windows because... why?