On page 11 and 12 of this document: http://www.theguardian.com/world/interactive/2013/oct/04/egotistical-giraffe-nsa-tor-document
they say it's easy to dinstinguish Tor users from non-Tor users because of Torbutton. They are probably using some user-agent+javascript stuff. But still, if someone wants to distinguish Tor users from non-Tor users, why not look up their IP address? If the IP is from an exit node, then we have a Tor user! Why do you think they aren't looking at the problem that way? Or I'm missing something..