[XorNot]

Pen register metadata was deemed not protected by the Supreme Court, but privacy rights still protect the content of most communications from seizure without a warrant.

It all comes down to reasonable expectation: to send a letter, or make a phone call, you obviously have to tell the phone company the details of who you're calling. Therefore the information is not considered to have a reasonable expectation of privacy. Whereas you don't need to convey the content of your email or voice conversations to them for the service to operate - you could scramble your voice, or encrypt your email, and it wouldn't change a thing.