I clicked on your profile and I assume you are referring to your website http://woobius.com ? I didn't try it out but I did checkout the screenshots. See, to me, your app looks like a web application. It borrows some of the visual metaphors of a desktop app, but the actual interface skin looks very much to me like a web app.
To take Jeff's metaphor, your app to me is like a C3PO. He's got all of the functionality and parts of a human (face, limbs, speech, etc.), but on the surface he looks like a robot, so it doesn't creep you out when he hobbles along with his stilted gait.
Anyhow, I thought the article was a bit long winded to make such a simple point, but for me the point resonated in the end.
For example, stupid cnnsi.com has a "main window" that has some things at the bottom that look, feel, and act like links. Yet I cannot middle click them to open them in a new tab. This annoys the bejesus out of me. Another example is desktop-emulating applications who don't have a fully-functional right-click menu like I'd expect.
By emulating other things, you put expectations into your user's mind about what sorts of functionality it should have. In this respect, it is analogous to the uncanny valley. The mimicry alone has created expectations that can cause frustration. But, that doesn't mean, that mimic'ing is inherently wrong or bad. It just means you have to do it right. You have to meet those user's new expectations.
In my experience the metaphor doesn't stretch to RIAs. My start-up's main application is precisely one of those "RIA that pretends to behave like a desktop app", and thanks to Flex we've been able to get a good enough approximation. Result? Our users don't feel uncomfortable about it (although we have had the odd user who seemed to expect that everything would be instant even though it was a web-app). On the contrary, our users love it, and have commented on it positively many times.
I guess people care less about that last 1% when looking at a web application than when looking at a humanoid robot. Which means stretching the metaphor in this direction doesn't quite work.