It's only a single factor if your password manager login is compromised. If you're instead the victim of a phishing attack or you somehow spill the password + an MFA token for a single service, then you still get some of the protections you would expect from MFA (e.g., the leaked login will be time-boxed and non-renewable).

To be honest, the most likely surface of attack for a user are database leaks. So long as your password manager is uncompromised, even if someone does manage to get ahold of your username/password for a specific site they won't get anywhere.