WebRTC being peer-to-peer, calls are encrypted end-to-end between peers. So if WhatsApp calls are peer-to-peer, then the call content would not be visible to WhatsApp/Facebook.

However, it's still possible to put a server between two participants so that instead of communicating directly, they would be communicating through this intermediate endpoint which would have access to call content - without call participants even knowing. So ultimately it's a question of trusting a particular service, not the protocol used.