That's why we have separate legislative, executive and judicial systems. That's why the Constitution specifically protects freedom of speech and the press and restricts searches and seizures. It puts limits on the government's right to root around in your life. If the government wants to search John Doe's snail-mail, it doesn't rifle through every letter that passes through Doe's local post office. The investigators never see the rest.
People subpoena e-mail records all the time.
The ISP has to comply. But the government claims that's too slow and inefficient to keep up with today's cybercrooks. Instead, the FBI wants to put a box in the middle of the e-mail stream that has the capability to see everything that passes through it. Given the history of the FBI, there isn't a whole lot of trust lying around - on either end of the political spectrum. Think what J. Edgar Hoover would have done with Carnivore.