So you're saying that Safari for Mac is a commercial product, but Safari for Windows isn't? Apple develops Safari because a platform without a free, high quality web browser just isn't viable, but that doesn't make Safari "commercial." I certainly don't buy the idea that Safari drives Mac sales.
But this is just nit-picking. I agree that the Times is being completely ridiculous here. There are all sorts of commercial entities involved in people reading the Times RSS feeds - Apple, Pulse, the users' ISP, the Times' hosting company, various telcos in between the two, the folks who made the routers the packets pass through, etc. The Times doesn't seem to have accepted that they don't have direct contact with their readers online; they're just one part of a larger ecosystem.
I agree it's a stretch demonstrating the absurdity of the NYT demand. Safari for OSX is a commercial product because it comes bundled with OSX and there is no other way to get a Safari to run on a Mac without buying OSX. In the case of Safari 5, you have even would have to buy 10.5 or 10.6.
Safari for Windows is just an attempt to get Windows web developers to test against Safari. No Windows user I know of uses Safari as the main browser.