The whole beauty of USB ports is that we have one unified interface for practically everything. It can't be safe without giving that up, adding some friction to user interaction, or doing some dark art involving centrally signed devices that we expect won't be broken. If anybody can produce storage and input devices that plug into a universal port and just work, malicious input devices can be made to physically look like storage devices in the eyes of the user. I'm not saying we shouldn't make more security conscious tradeoffs, I'm just saying that there are tradeoffs to be made, and most users probably won't appreciate the added friction.