With a keylogger, you lose passwords you typed in since the keylogger was installed, but that is rarely all of your passwords.
This still leaves a case where someone manages to get the final key out of memory but you're pretty hosed at that point anyway. I'd prefer a system where the yubikey itself is doing the final credential decryption instead of the CPU, unfortunately most people aren't that paranoid though.
I’ll stick to passwords that are impossible to guess and an encrypted vault with multifactor authentication.