I don't find an essay by Professor Bérubé titled "Paying for Freedom." I do find an essay titled "What Does 'Academic Freedom' Mean?" (2006) in which he speaks of the idea that academic freedom is being threatened by those who think they can control that freedom by paying for it.
If this is the essay you speak of, I can discuss two points that are important--and highly contentious--that Bérubé advocates in this essay about academic freedom. Academic freedom, a concept sprung from the Enlightenment period, is the freedom of scholars to research and teach without control or restriction from governing bodies or religious overseers, such freedom as Galileo did not have. This freedom does much to assure that results of research and that teaching the results will be free from preconceived and biased approaches and results. This is what Bérubé is for in his writing: he champions traditional academic freedom.
Bérubé points out that in contemporary America local legislating bodies are attempting to pass bills that require government oversight of academic hiring and teaching. This, according to the Enlightenment tradition, entirely violates academic freedom. The justification put forth by these advocates of intervention from government into the freedom of academia is that if public taxes pay for public education, then public regulation is right and justifiable. Yet, according to Bérubé, with current costs, local taxes pay only a small portion of academic budgets. This is what Bérubé essay is not for: he opposes any such intervention. Bérubé explains the idea this way:
The argument goes like this: we pay the bills for these proselytizing faculty liberals, so we should have some say over what they teach and how they teach it. Public universities should be accountable to the public. [...] people who say, in effect, “I pay 10 percent of your salary, and that gives me the right to screen 100 percent of your thoughts.”