Comparison of Secure Messaging Applications

What I can not comprehend is how respectable people and experts like Snowden and others from EFF can get behind a messenger that its authentication is based on cell phone numbers!

When an application sends all your contacts to its servers (whether they are hashed or not) and more importantly when your whole access depends on a none encrypted code sent via SMS and worst of all, your identifier can be tied to your real identity extremely easy, how can they call it secure at all?

It is not all about E2E or how the crypto is designed or implemented, its also about your anonymity, your social graph and other pieces of information which are arguably more important not to give away!