Federal Agents Pierce Tor Web-Anonymity Tool (online.wsj.com)

That's a terrible article. The only concrete example? A postal inspector found some dubious physical mail that led to a suspect.

Do spies and other secret agents use Tor?

I've always assumed it was developed mainly for them to use, because a US government VPN would be too obvious.

If Tor wasn't public then a could just say, look, there's a US spy at this IP because they're the only person using onion routing.

These are it's weaknesses http://en.wikipedia.org/wiki/Tor_(anonymity_network)#Weaknes...

Also I think Harvard caught a student who reported a bomb threat over Tor, but was caught because there was only one student using Tor on the Harvard network at the time, oops.

http://www.businessinsider.com/harvard-student-used-tor-for-...