But even encryption can be cracked in certain cases (weak protocol, weak passwords, back security practices). However if everyone started to encrypt most of what they do online, then agencies would end up with a massive amount of encrypted data that would take huge amounts of money, time and computing power to attempt to crack. However most users are too lazy, and they just want shiny apps with bells and whistles, that "just work".
As far as secure IM is concerned, I decided to set up my own Jabber server for my friends and family with enforced encryption. Hardly anyone showed interest though, they would much rather continue using Skype and Whatsapp & Co because they don't require the user to think.
To understand how PRISM works check out the podcast on the Security Now episode #408 "The State of Surveillance (How the NSA's PRISM program works.)": https://www.grc.com/securitynow.htm