Unless a company is specifically geared around a toolset that doesn't exist in OS X or *nix (game developers come to mind), institutional, mandatory Windows use seems like a great signal for "shitty company right here!".
I mean, imagine telling someone you don't like their cooking and then saying "The fact that you use margarine instead of butter says a lot." You're not directly saying anything bad about them personally, but most likely they're going to take it as a roundabout way of saying "Real cooks use butter, but you use margarine. Therefore, you're not a real cook."
So what if he did? By the time you've reached that point you really ought to have figured out the entire post is a subjective opinion.
Here, I'll say it too: I don't want to work for an organization that primarily runs Windows by default. I don't have to justify it rigorously scientifically. Nor am I saying there are no skilled Windows developers in the world. In fact my company has quite a few in it ("some of my best friends are Windows developers", ahem). Nevertheless, I do not want to work for a primarily Windows company. I do not like Windows software culture.
That's when you say "I'm not a Windows guy" and leave it at that.