I'm reluctant to jump on this bandwagon as I don't feel that Tor is as secure as they say. There have already been demonstrated attacks against node anonymity and until Tor gets a public audit I'm not sure it's wise to encourage people to use Tor.
As they say, flawed crypto is worse than no crypto at all.
You're right that there have been demonstrated attacks as well as many "theoretical" ones. Interestingly, many of the theoretical attacks become even less theoretical when the number of exit nodes (and, in some cases, even middle relays) goes up. An increased number of end users using the Tor network also decreases the chances of many of them being successful.
Perhaps someone should start a fundraiser for an audit of Tor. I would certainly toss a few dollars into the jar for that myself and I suspect sufficient funds could be raised pretty easily.
As they say, flawed crypto is worse than no crypto at all.