Personally I couldnt really care less. People will use what theyre confortable with and/or enjoy and good luck to them for that. Surely an amiga based site and it's people understand that ? As for why Windows is so dominant, there's plenty of reasons. Firstly (besides marketting) it's software. As good as some open source software has become, for the most part it's inferior to dedicated commercial efforts (with obvious reason).
Firefox, Google Chrome (combined 43% of market share) and Apache (58% of server market) seems to disagree with you.
You are misunderstanding how software works, though.
The operating system and the software you run on it have nothing to do with each other. You can use proprietary software on linux (I own Quake wars and Prey f.x.) and you can use open source software on windows (firefox f.x.)
Also, and Im sure long time linux users might disagree as they've by now learned how it works, but Linux simply isnt as friendly, even the more popular distros arent as easy to get your head around as Windows.
Take two people with no previous computer experience and sit one in front of a linux machine, and one in front of a windows machine. I'll guarantee there'll be no difference in their ability to do their daily stuff. Why would there? Either way, you are just clicking on icons.
Windows is familiar because you've already used it, not because there's somehow anything more intuitive or helpful about it. (if you don't believe me, google "windows troubleshooting" or similar and see how many millions of hits you get.
Will linux ever "rule" the desktop ?
No more than amiga ever would have ruled it.
Does it matter ?
No. The choice is there for those who want it (stability, freedom). The desktop is only one tiny bit of what linux is, can and does.