From the article:

....Chomsky has never hidden the fact that his university, the Massachusetts Institute of Technology, was “about 90% Pentagon funded”. As he says of MIT in the 1960s: “I was in a military lab. If you take a look at my early publications, they all say something about Air Force, Navy, and so on, because I was in a military lab, the Research Lab for Electronics

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MIT etc. get a significant amount of their funding directly and indirectly from the government (and the different tentacles of it). It is natural that they serve their sponsors and benefactors. You can never be truly independent of who pays your bills.

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Again from the article:

CHOMSKY’S POLITICS

As part of this activism, Chomsky advocated the “avoidance of work that can be used by the agencies of militarism.” He also gave considerable thought to “resigning from MIT, which is, more than any other university, associated with activities of the Department of ‘Defense’.”[26] But MIT’s managers had treated him particularly well, making him associate professor at the age of 29 and a named professor at 37. And, as Chomsky says, this named professorship, which he received in 1966, “isolated me from the alumni and government pressures.”[27] Consequently, he was now in the rare situation of being free to be an outspoken anti-militarist while still working for one of the US’s most prestigious military labs.

Such a situation had many advantages, including the fact that such proximity to the US’s military and scientific elite gave his criticisms of that elite a unique authority. But to be the Pentagon’s No.1 critic while remaining loyal to the Pentagon’s No.1 university was never going to be straightforward. It led Chomsky to take a variety of contradictory positions on events both at MIT and in the wider world.

For example, despite his sympathies with their anti-militarism, when student radicals protested against MIT’s military research in 1969, Chomsky apparently stood in the MIT President’s office to help loyal staff protect it from being occupied by these same radicals.[28] Then, when Walt Rostow tried to return to his former job at MIT, Chomsky threatened to “protest publicly” in favor of Rostow being allowed back to the university. According to Chomsky, Rostow’s leading role in the Vietnam War made him a “war criminal”. But Chomsky was quite open about the fact that he “supported the rights of American war criminals not only to speak and teach but also to conduct their research, on grounds of academic freedom, at a time when their work was being used to murder and destroy.”[29]

Commentators have usually seen Chomsky’s attitude to war research as just an example of his uncompromising commitment to academic freedom. But we can now see such comments in a different light, as an attempt by Chomsky to come to terms with his own early career decisions at MIT. The same might be said of Chomsky’s defense of Robert Faurisson, the French academic who was deprived of his teaching job after he wrote a book denying the Holocaust. Clearly Chomsky has never had any sympathy with Holocaust denial. But if academics should be free to produce work that enables the military to “murder and destroy,” why shouldn’t they also be free to promote Holocaust denial?