D. A. Carson has a great book out called The Intolerance of Tolerance (also available in paperback). Carson explains how the current mantra of tolerance is simply an excuse to be not just intolerant but tyrannical. I noticed in graduate school, both at Berkeley, and even more so at Yale, that an immense amount of bigotry was promoted in the name of intolerance. Carson provides many examples of the intellectual vacuousness and hypocrisy promoted in the name of tolerance. He also distinguishes between two different philosophical positions promoted under the name of tolerance and argues that one should be supported and the other thwarted.
I highly recommend the book. It should be required reading, especially at Ivy League schools.