Stephen Hicks offers a very good defense of academic freedom in his article, "Free Speech and Postmodernism" in the current edition of The Navigator. A sample:

It is therefore surprising that the greatest current threats to free speech come from within our colleges and universities. Traditionally, a major career goal for most academics has been to get tenure, so that one can say whatever he wants without being fired. That is exactly the point of tenure: to protect freedom of thought and expression. Yet today we see that many individuals who have worked for many years to get tenure and the academic freedom that goes with it are the strongest advocates of limiting the speech of others.

The whole piece deserves careful reading.