How do you link your hardware key to the website? You still have to plug it into a proprietary black box.

If you think your computer security is weak, it will continue to be the weak link even with with a hardware key.

If the computer is compromised or backdoored, it will have access to private keys for websites that I access on that computer, one per each touch, not the database of all private keys. For example, I may not connect my Yubikey to some computers at all.

Hardware keys are made not to give out secret keys without physical touch.

Firmware in Yubikey is not updated, unlike over the air phone update.