I don’t know much about the funding, but I don’t have any doubts that Nick Gillespie at Reason and David Boaz at Cato are certainly true libertarians. They may not go as far as some anarcho-capitalists and others might like, but they’re definitely not closet statists.
It’s interesting, I was reminded of my own journey into libertarianism when I came across this recent thread. I actually discovered Cato and Reason before the LvMI. And even then, it took me quite some time to get deep enough to unearth the in-fighting among these major libertarian forces. It was quite sad and disheartening to see, as I’m sure we’ll get at least a few illustrations of it here. In some respects there is some animosity (mostly between a few select individuals associated with Cato and individuals associated with LvMI), and that tends to lead people into making blanket statements about entire organizations and those who affiliate with them. I actually don’t recall ever hearing or seeing Reason being brought into it, but I have certainly seen a couple of things published on the website that I couldn’t believe got written at all, let alone okay-ed by the powers that be. (e.g. this one, which, if you read even a fraction of the comments, you’ll notice was not well-received at all. And it gets even worse when you get to the asshole author’s asshole response to the comments he was getting. That actually got me to write in and share my disgust with the powers that be at the foundation.)
But to get to your question, no, by and large I do not believe Cato or Reason are faux libertarian fronts for statist corporate interests. I don’t know much about the character of the Kochs, but I’ve seen enough from both of those organizations to assess that their fight is genuine. And while, as I said, some may not find it libertarian enough, I still find it to be geniune liberatarian.