The claim is that "massive funding from the U.S. government, the Pentagon and the national security state."
The first part is based on the fact that University of Minnesota, Georgia Tech and Princeton University, and Georgetown are funding the tor project. The argument is that all of them are receiving their money from the U.S. Government, and even if they claim that they are independent organization they are just fronts used by the government when it comes to funding the tor project. One could also get the impression that the U.S. Government are the only source of funding for those universities, and that the universities gets no research funding elsewhere, demand no tuition from students, and so on.
The Pentagon claim is likely derived from statements that SRI international is a sponsor of the tor project, and they receive funds from US Department of Defense. Again, one must assume that SRI international only gets fund from a single source.
I can only guess that the national security state is a reference to either the U.S. (ie, the above), or the Federal Foreign Office of Germany, or US Department of State Bureau of Democracy, Human Rights, and Labor.
The cited Guardian source is based on 2013 financial report, and the list of sponsor today is naturally quite different, but I guess thats not an issue.