They're not the same thing, i.e. I use protonmail exclusively WITH Thunderbird. Thunderbird is an email CLIENT, and as long as you configure it correctly, doesn't care whether it's pulling/sending messages from/to a hotmail/gmail/yahoo mail/America Online/protonmail et c. server. Protonmail is an email sever that HAS a web interface, but like you I prefer Thunderbird's. So I use protonmail for its secure servers and Thunderbird as my email and calendar client.
I hope that clears things up.