I'm no expert on these sorts of things, but it seems like the story goes something like this: 1. Dev checks out his site using IE 2. Dev realizes that IE users were getting scary warnings about his software 3. Dev has to pay up money to a third company to make the scary warnings go away. Seems like a bad state of affairs to me.
I suppose if you're selling to the Windows market, the App Store will be required in a few years as Metro becomes the dominant Windows UI (and Metro apps have to be sold in the Microsoft App Store).