This week as Silk Road is raided and billions in Bitcoins are taken in by the FBI, representatives for the secure internet system known as Tor have stepped up to suggest that the government did not break down security in Tor itself. Instead, they say, the FBI found out the Silk Road network and took them in using regular old "actual detective work." Tor also suggests that they've only known what's going on with Silk Road "by reading the same new sources everyone else is reading."
It's been suggested by representatives for Tor that they've been investigating themselves to see if any "flaws with Tor" were at fault for this situation and if there's anything they need to correct. At the moment, it would seem that Tor is still just as uncompromisable as ever. The software and the network known as Tor remains secure.
The team at Tor has pointed the users of their network and software to the Tor warnings list which suggests users only work with the official Tor Borwser, use HTTPS versions of websites, and refrain from opening or installing browser plugins. They also suggest that no downloaded documents be opened while users remain online, and that users tune in with bridges and/or find company.
"Also, while we've seen no evidence that this case involved breaking into the webserver behind the hidden service, we should take this opportunity to emphasize that Tor's hidden service feature (a way to publish and access content anonymously) won't keep someone anonymous when paired with unsafe software or unsafe behavior. It is up to the publisher to choose and configure server software that is resistant to attacks. Mistakes in configuring or maintaining a hidden service website can compromise the publisher's anonymity independent of Tor." - Tor
As far as those involved with running Tor can tell, the FBI's suggestion is true: that their suspect "made mistakes in operational security" - this suggesting, again, that Tor's protocols were not in any way at fault.