I always like to remind people that Tor is funded by the USG (currently, actively). I think it's very important that people understand that and adjust their threat models based on that.
However, it's not all bad news ... in fact, I think there's a very significant upside to the USG funding of Tor:
It provides a very compelling defense in the event that simply participating in Tor begins to be prosecuted.
There is very often a worry put forth that simply participating in Tor (as a client or by running a relay, etc.) can in itself be considered an illegal act. I think that as long as the USG is funding the development, people in the US can rest easy that they can't be prosecuted in any way for simply participating on the Tor network.
"If the USG is funding it and the state department is encouraging people to use it (think arab spring) then how could my use of it be illegal ?"
IANAL.