They first called it Windows because it had... Windows... Now the Windows name stands on it's own as a Microsoft brand, and nobody thinks of it as "that computer operating system that has *gasp* windows...", therefore we don't need a visual to remind us of, windows.
This really showcases the utter lack of soul and creativity at Microsoft. They could make it look like anything they want now, even hired a reknowned artist to make a beautiful original logo, but instead they let Steve Balmer's 10 y/o son make the logo in 5 minutes with MS Paint.
Heck, I'll admit that my only graphics design skill is photoshopping people's heads onto different bodies, but even I could've came up with that logo, or quite possibly even a better one.