It makes more sense once you realize things like Tor were created specifically for the USG intelligence community[1]. Bitcoin could, for example, be used to trade money between drug traffickers and the CIA, whilst allowing DEA to track the funds around the world. Fun!
The Navy was originally interested in techniques for decentralized communication between ships in a fleet, in such a way that the flagship would be unidentifiable. There are lots of applications for such a network that different government organizations would be interested in; The Government isn't a monolithic entity.