"Tor was not started by the US Navy. The US Naval Research Labs (NRL) started a project in the 1990s called onion routing7. Tor uses the basic onion routing principles and applies them to the Internet. The volunteer Tor group started in 2001. The formal charity, The Tor Project, started in 2006. We continue to work with Dr. Paul Syverson from NRL on improving onion routing and therefore Tor."
If you ignore some of the drama, Pando has a very long and fairly comprehensive look at its funding (at least, it seemed comprehensive to me, I am not a Tor expert) - http://pando.com/2014/07/16/tor-spooks/
Yes, the government funds Tor. Pando thinks that all of the US government is akin to the NSA and wants to spy on people. This is not how it works. The government is not just one body and there are many parts of it that probably don't agree with what the NSA is doing.
Yes Tor is funded by the US government. My question is, how does it matter? The protocol is open. The code is open. There are research groups at some major universities researching on Tor.
Let the code speak, not fear mongering.
This, I think, is a very important point. It is beyond naive to assume that a large body of structures that together are called "the US government" is a homogeneous entity that can be ascribed goals as if it were a single agent.
There is a very widespread and dangerous misconception that Tor is a one-stop shop for secure or anonymous communication. This is not true. You need to encrypt your messages separately. When outside the onion network, Tor actually exposes all content sent through it to a third-party, the exit node. This means using Tor may be more dangerous than not using Tor if you don't know what you're doing.
Source: https://www.torproject.org/about/overview