The point of the article is that you are damned if you do and damned if you don't. If you don't encrypt transmissions, whether they are emails, instant messages or whatever else, you are subject to spying, and your transmissions are sent in plain text, VoIP, or whatever. If you do encrypt said transmissions, it's a "reason" to suspect you of "unauthorized" activity. The encrypted traffic captured is held forever, or until the NSA can decrypt it to look at the contents.
It's a no-win situation.