You are missing the point. The point isn't that e-mail isn't a secure form of communication. The point is the NSA is capturing ALL of it and storing it in massive data stores. The NSA can search through ALL of the captured data at will. That US Federal government have the e-mails. There is really nothing in place that prevents the government from search through the stored data time and time again for years, except for some "rules".
The fact the government CAN search through your e-mails at will is what PJ is concerned about. She a very bright person. She's gone over the issue in her mind. She realizes all of the ramifications of the government capabilities of the NSA. And it scares the hell out of her. It's created a chilling effect on First Amendment rights. Lavabit, Circle Mail, Groklaw are just the first visiable causalities of this chilling effect on free speech. And it's going to get worse and worse as more people realize the full impact of what the Snowden leaks are telling us.