Despite the title, this article isn't aimed at people looking for general-purpose private/secure communication. It's specifically for those who want to torrent pirated music/movies/tv, but do not want to leave any way for a subpoena from the US government to reveal their contact information. The goal isn't just privacy, but anonymity.
VPNs still work perfectly for private/secure communication, as long as you trust whoever's on the other end -- for most people, this is their employer.
For those who truly do need to be anonymous, Tor is still the standard. It doesn't work if you need to transfer terabytes of data anonymously, but it's fine for browsing or small-scale file exchange (eg wikileaks).
VPNs still work perfectly for private/secure communication, as long as you trust whoever's on the other end -- for most people, this is their employer.
For those who truly do need to be anonymous, Tor is still the standard. It doesn't work if you need to transfer terabytes of data anonymously, but it's fine for browsing or small-scale file exchange (eg wikileaks).