You are comparing two different things. Email is a generic concept - it's not proprietary . A message sent through Whatsapp is an instance of the whatsapp application - not a standard message.
Basically, if we push your analysis further, Facebook, which is a communication application, should let you send a message to your twitter account, that you could read with twitter, and reply with a comment on an Instagram picture. That'd be the same thing - I mean, they are all "messages" somehow, aren't they? See, it's - as you say - clearly idiotic as no one would open its platform that much.
> Email is a generic concept - it's not proprietary
Concepts can't be proprietary altogether. You can't own ideas. Instant messaging isn't proprietary either.
> A message sent through Whatsapp is an instance of the whatsapp application - not a standard message.
If you are talking about certain implementation of ideas being proprietary - that's exactly the point of my original comment. Making it intentionally incompatible to "control the market" is crooked lock-in tactic. Which is especially the case with Whatsapp which internally uses XMPP which was designed for interoperability and as IETF standard.
And I brought examples with e-mail. A long time ago Compuserve and AOL e-mail services used to be incompatible on purpose. But pressure from users to end that stupidity forced them to reconsider. There is no valid reason that a lot of IM services can't interoperate to a good degree. Except for greed and backwards thinking.