Historically the university engineering and science departments have always done military research. Not exclusivly, of course, but when you need to raise money to pay for the new equipment, you go where teh money is.
It's the political science and other humanities students that were doing the protesting.
During the 60's a tiny few of the more radical activists even went as far as bombing the research labs. But the labs they were bombing were still part of the campus and staffed primarily by other students and professors.