So that's not good. You can see how that could be happening; NSA has trunk-level access to telephony circuits. Telcos are engaged in a long-running game of footsie with the government that makes billion dollar Internet companies look like anarcho-capitalists. But I'm not seeing how we get from there to the contents of email. To have the email of arbitrary Americans without a warrant, the NSA would need direct access…
But I'd be very reluctant to conclude that the NSA doesn't have clear-text for the vast majority of email that gets sent.
Google and other email providers have denied giving the NSA access to their servers, but if you think about it, that would be a lousy way to share data with the NSA, from a purely technical point of view. A company like Google is going to be constantly evolving their infrastructure. Giving the NSA direct access to the servers hampers that, because they'd have to break compatibility with whatever client software the NSA is using. It'd be easier to just send copies of all email that moves in and out of their system to the NSA and let them sort out how to process it. That would be more convenient for the NSA too.
Beyond that, all the denials issued by Google, Facebook et al mention that they do provide the government with information as required by law. We know that there are secret laws at work here, and if the law requires companies hand over everything, then that's what they're doing. The may even be required to lie about it. They're definitely absolved of any legal liability for doing so. I don't doubt that internet companies try to protect their user' privacy as much as they can, but that may amount to "not at all" where the U.S government is concerned.