From the article, emphasis mine:
...the operators used software provided by the TOR Project that makes it virtually impossible to track the activities of users' IP addresses. The alleged conspirators also used IP anonymizers and covert currency transactions to cover their tracks. The indictment, which cited e-mails sent among the men dating back to 2006, didn't say how investigators managed to infiltrate the site or link it to the individuals accused of running it.
I'm willing to bet that money transfers and the transfer of goods sold are still far more discoverable than individual Tor users but any assurances of that would certainly be welcome. I hope the Tor Project will be forthcoming with some as soon as some technically useful info is available.
They use bitcoin. The security reaches only as far as bitcoins security. You can hide behind an IP in the middle of the red sea if you wanted. If your bitcoin transaction can be tracked, you bet your ass you can be tracked as well.
When you don't know what to do, walk fast and look worried.
