Earlier quoted context omitted.
"We kill people based on metadata" ~~ General Michael Hayden, former director of the NSA
Yeah but he was referring to direct phone contacts. You connecting to a Skype or Facebook server doesn’t tell you anything.
Lets say someone is using a northern european vpn-server to connect to facebook and that vpn-server is not cooperating. Decloaking is statistical analysis against timing and rough size of packages, so tapping the cables on both ends of the vpn-server and recording metadata for all its connections is key, even if they can't break the encryption.