Messengers encrypt YOU!
Being a Russian I just don't beeping care. And maybe I'm even glad that this bill is proposed, because it means that all the official messengers (I mean: companies that provide messenger services using closed source software) will be compromised and the only messengers that are trustworthy will be the open source decentralized ones having no central authority that can be fined.
In such conditions the maximum fine would be 5000 Roubles (less than US$100) which means that the expense of collecting the evidence would not pay up. It's just impossible to interrogate everybody whose traffic comes to some nonstandard port, and it's impossible to prove that it's a messenger and not anything else.
Also I hope that any software that used the outdated HTTP(S) and HTML protocols which have so many builtin security holes will be compromised at last and the only programs that survive would have no such thing as web page phenomenon and correspondingly site phenomenon. For instance, Freenet now supports something like a webpage. But it edits out anything that could be dangerous. RetroShare just has no web page. It displays web links but you should copy them to the browser with full understanding for your actions.
Please understand: This bill is neither Putin's nor the FSB/KGB initiative. The FSB works stealthly. It's the initiative of parlamentaries who propose the laws that just cannot be observed.