That's the crux of the matter, Ian. The MIT funded his work on linguistics for decades...they wouldn't have done that had his theories not been compatible with the military-industrial complex.
I saw Chomsky speak twice in the same week when I lived in London years ago. He spoke at 'The Rebellious Media Conference' where the audience were mostly activists and a lot of anarchists were there. He seemed ill at ease, a bit rushed and irritated by some of the questions. A few days later he had a lecture at Kings College London on Geopolitics (Changing contours of World Order, or something) but he was sharp, in a good mood, flowing, articulate, his encyclepedic knowledge on full display...much more at home in an academic setting amongst academic types. Might've been that he was still jet-lagged at the first talk but the difference was night and day and always stuck with me.