The article is in response to a dragnet surveillance program, where everyone's communications are watched and presumably datamined. It's very easy to do this, because nothing is encrypted, and everyone uses services that expose metadata (like who is IM'ing who).
Your comment is entirely true. However, it presents an adversary that doesn't want dragnet, but targeted surveillance. It assumes that Bob will be immediately arrested if his communications become encrypted.
This is not the threat model that we're faced with now. Let's say you and Bob communicate using accounts you've made on random XMPP servers using Tor, and all the messages are encrypted with OTR. Both servers are in the US, and the NSA's metadata database shows E83Gxw@jabber.org sending lots of ciphertext to PAnd9B@jabber.org.
This is "NSA-proof" in that the NSA would not know to link PAnd9B@jabber.org with you using their existing systems. They would have to drastically escalate the cost of their surveillance program with respect to you and Bob to figure out what you're talking about. Unless you really are a political dissident, conspiracy theorist who accidentally discovered the UN's black helicopter program, or radical Islamist, you are now out of the surveillance dragnet.
That is to say, unless the threat model changes, using privacy-enhancing technology will keep your data safe from PRISM and similar dragnet programs.