However in this particular case, even the security argument doesn't hold, either I:
a) know that I want to use USB - in that case I'll switch browsers or download a native binary (even more unsafe), it's not that I'd decide that I no longer want to flash my smartphone
b) I don't understand what's happening but I follow arbitrary instructions anyway - WebUSB changes nothing.
A 0day in a browser for the WebUSB system would allow any website to mess with arbitrary USB devices connected to your computer.
While the browser sandbox is generally safe, it is also a huge target, and with a security risk like that, it wouldn't surprise me if it's a prime target for black hats.