Mixnets like Tor generally aren't considered secure against an adversary who's monitoring the whole network. Maybe the NSA isn't there quite yet, but they're sure trying. If they succeed, a DC-Net can still provide perfect anonymous communications, but it's hard to make those scale. There's been some work to improve matters, eg: https://www.usenix.org/conference/osdi12/strong-scalable-ano...
I may be ignorant, but doesn't it take a lot of statistical analysis to do attacks like this? The point being not that the NSA cannot do it, but that they have to be specifically targeting you to pull it off. Unless they know what's going through the wire, how will they know to target you?
Edit: also this (pdf): http://secan-lab.uni.lu/images/stories/christian_franck/FRAN...