This reminds me of an old interview with Linus saying that while he thought the Windows logo was ok (he might have said good, I don't remember), you can't really do anything with it, while you can do put Tux is all sort of situations. It was quite common to see him playing ice hockey or reading a book or whatever -- if you knew the logo (Tux) you knew it was Linux-related.
In contrast, Tux seems a bit stuck. It's going to be hard to make him anything but cute and cuddly. A more stylized penguin would look cold and sinister.
I can honestly say, I've never looked at the logo and thought "Hey! That's a window." But that's just me.
I did a google image search for 'Tux' - I think it demonstrates the versatility of having a living character as a logo. You can put him in lots of different situations and it's still clear that he's the 'Linux Penguin'.
http://people.mozilla.com/~faaborg/files/20090515-evolvingPr...
Ironically from a good article on mozilla.com, talking about how they're evolving the Firefox icon:
http://blog.mozilla.com/faaborg/2009/05/14/evolving-a-produc...
Of the examples they give Windows is notable as being the logo which has undergone the most significant changes (while still remaining recognisable).
I smell a photoshop contest.
Whether this proves or disproves the point probably depends more on your personal definition of "cute and cuddly".
I can't picture the Windows logo playing hockey. It doesn't even have legs. (I can picture Clippy, though. Argh.)