You have a point, I would be stupid not to agree the it's probably mostly infected Windows machines. I just don't think that's what the summary is saying. When the text of the link to the article says "how vulnerable Windows XP really is", i read it as that, not as "how many infected Windows XP boxes are out there."
The point of the article, IMO at least, is to remind people how quickly an unpatched Windows machine gets infected and therefore how important it is to keep your OS updated. That they used an updated "secured" Windows installation to host the virtual machine sort of shows this, I would say. I just think simply saying "Windows XP is unsecure" is not really what this article is trying to say and that the summary was a bit too simple in that sense.
And just to make it clear, I'm posting this from my Ubuntu laptop. I've been running Linux exclusively for around 5 years (non-exclusively for around 8), so I'm far from an MS fanboy. I just think with all the reasons there are for critisising MS and Windows, there's no reason to make this just another "Windows is insecure" story.