Bear in mind the US Govt invented both the internet (more anonymous/decentralized than AOL/Compuserve), and Tor. Governments are big and are full of people with differing priorities.
If most BitCoin usage is legal I think it'll be OK in the long run. This is why I wish we'd kick the people selling serial keys and the Silk Road guys out of the forum. Of course they can still do what they're doing, but there's no need to advertise them in the main forum.
Bear in mind that the government only does things for it's own benefit. The internet was created AFAIK to allow a more efficient, less centralised, and robust command and control system that could withstand a nuclear attack.
Tor was created specifically so that U.S. spies could safely communicate, and send messages while being in hostile territory without being compromised.