Concerning whether Tor networks might or might not be compromised trojan horses:

Reason why it might be: 80% of the Tor Project's $2M annual budget comes from the United States government (says wiki), this perhaps implies that the US gov. has some influence or control over what goes into Tor, and so if there's anyone who knows how to identify Tor users, it's the US gov.

Reason why it might not be: Snowden had Tor stickers on his laptop, that sort of lends credence to the fact that NSA doesn't have it down yet on how to id Tor users and it is still a good and reliable anonymity tool.