My problem is how they portray this. Direct from the article:
"The highly classified program, code-named PRISM, "
and also:
"The technology companies, which participate knowingly in PRISM operations, include most of the dominant global players of Silicon Valley."
If you have numerous (non-government contractor type) companies knowingly participating in the program, then it isn't "highly classified." And if you thought that your communications were private then you were fooling yourself. Even Tor, the darling of the EFF, was initially developed by the Navy. It's very tough for people to communicate electronically these days without the government being able to listen in.