One of Tor's weaknesses has always been the exit node problem, where things can be seen in the clear unless encryption is used. And sometimes it's not used, so personal data can be gleaned through exits.
Another weakness is the Tor Browser Bundle itself. I'm not certain if it's 'compromised' but we'll never know, due to the secret nature of 0-days. People don't take extra caution and connect to Tor with a specialized Tor router with a kill-switch / fail-closed system, thereby mitigating real IP leaks.
There's also a more academic in nature problem of a 'bird's eye view' of the Tor network, whereby if you control and have insight into all the hops a Tor user makes, you can do correlation attacks, but I'm less concerned about that than the other two weaknesses I mentioned.