I'm a bit uncertain that document is completely credible - it makes some claims that appear to be very wild, even given what we've seen so far.
But let's assume they're right about their Tor claim. Even if the NSA places you on a controlled Tor network, I could still read my gmail because the NSA would have to try to get around Google's SSL.
Some bad endpoints have been known to try and MITM SSL before, but always with self signed certificates, so if the user messed up it was down to them.
Of course, if our endpoints are run by the NSA, and the NSA have pressured other CAs to sign *.google.com, we can only depend on cert pinning. But it's the NSA, so how do we know that they haven't already backdoored my browser to change the pinned fingerprints...
But at the end of the day, the latest I'd heard from the Snowden revelations is that Tor is a major thorn in the NSA's side, so I'm inclined to believe that over this breathless PDF that makes all sorts of outlandish claims.
EDIT: From that PDF:
> When the DSL connection is established a covert DHCP request is sent to a secret military network owned by the U.S. Government D.O.D. You are then part of that U.S. D.O.D. military network, this happens even before you have been assigned your public IP address from your actual ISP.
That stretches the bounds of credulity - it assumes that a giant government-mandated conspiracy exists between ISPs, device manufacturers, networking developers... even with what we've seen so far it's impossible to swallow.