It’s true that the Windows logo has long looked like a waving flag, which makes absolutely no sense. And the new logo is better. But it brings up a bigger question: why is it still called “Windows” at all?
Yes, the desktop variety will still have windows. But the mobile/tablet variety is geared towards the “tile”-style of Metro. In fact, as Moreau points out, Metro heavily influenced the new logo design.
I actually think “Windows” makes as much sense now as it ever has. When you look at the tiles, they feel a lot like windows. Each of them is a window into an application. The concept of what a window is has changed, but it’s still there.