There are a lot of different theories on why this is so and what, if anything, should be done about it.
One theory for the scarcity of Republican professors is that conservatives are simply not that interested in academic careers. A Democrat on the Berkeley faculty, George P. Lakoff, who teaches linguistics and is the author of "Moral Politics: How Liberals and Conservatives Think," said that liberals choose academic fields that fit their world views. "Unlike conservatives," he said, "they believe in working for the public good and social justice, as well as knowledge and art for their own sake, which are what the humanities and social sciences are about."The other side of that theory would be that conservatives are less likely to have a problem with trying to make a lot of money, which causes academia to fall in their ranking of preferred options. Then there's this reference to The Federalist Papers:
Some non-Democrats prefer to attribute the imbalance to the structure of academia, which allows hiring decisions and research agendas to be determined by small, independent groups of scholars. These fiefs, the critics say, suffer from a problem described in The Federalist Papers: an autonomous "small republic" is prone to be dominated by a cohesive faction that uses majority voting to "outnumber and oppress the rest," in Madison's words.
It doesn't need to be a nefarious desire to oppress the minority here.
Martin Trow, an emeritus professor of public policy at Berkeley who was chairman of the faculty senate and director of the Center for Studies in Higher Education, said that professors tried not to discriminate in hiring based on politics, but that their perspective could be warped because so many colleagues shared their ideology.
"Their view comes to be seen not as a political preference but what decent, intelligent human beings believe," said Dr. Trow, who calls himself a conservative. "Debate is stifled, and conservatives either go in the closet or get to be seen as slightly kooky. So if a committee is trying to decide between three well-qualified candidates, it may exclude the conservative because he seems like someone who has poor judgment."
It's an ancient human foible to think people who don't agree with you must be uninformed or dumb.
UPDATE: The Times points us to a website where you can read the details of the study. And contrary to what I wrote above, the Times did have a bit of information about where the Republicans were clustered: "The ratio of Democratic to Republican professors ranged from 3 to 1 among economists to 30 to 1 among anthropologists." Looking at the survey itself, you'll see that it's 28 to 1 in Sociology, 13.5 to 1 in Philosophy, 9.5 to 1 in History, and 6.7 to 1 in Political Science.