This accompanying article has useful context: http://www.theguardian.com/world/2013/oct/04/nsa-gchq-attack...

> But the documents suggest that the fundamental security of the Tor service remains intact. One top-secret presentation, titled 'Tor Stinks', states: "We will never be able to de-anonymize all Tor users all the time." It continues: "With manual analysis we can de-anonymize a very small fraction of Tor users," and says the agency has had "no success de-anonymizing a user in response" to a specific request.

So only with "manual analysis" can intel agencies have any success, and that appears to be with a small subset of users who have other vulnerabilities. But when targeting a specific user, the NSA appears to have had no success in de-anonymizing them.