Well i flashed my board with the Asus Update on Vista and everything was ok. It is a matter of common sense to not have spyware and trojans and disable the antivirus software when doing an update.
As for the others that do it via usb driver, well you have to admit that with the Asus Update you get the latest bios available for your board, and there is also a point here because if you give the example with the guy that was updating the bios with antivirus software running i also can give an theoretical example of someone that downloaded the wrong bin file. So Asus Update pretty much solves the what bios file do i need question.
All i can say about the guys that update their bioses with Ezflash and other dos programs: CHICKEN . Lol,/joke.