Yes they're difference.
- Encryption mostly mean only protect the transport from e.g. user to Server
- password protection protect the data itself against unauthorized access as it's just plaintext without.
Best example:
Nowadays Email is transport protected so no (normal) attacker can read the content
But the email server from user side, the email server from receiver side and of course the receiver itself can read the mail without any special stuff as it's just plaintext