Jonathan Haidt, whose study on the dearth of conservatives in academia was the centerpiece of a John Tierney article I critiqued, says he's been swept up in a set of arguments he doesn't endorse:

My point was not that discrimination causes the underrepresentation. My point was that there is an underrepresentation of conservatives for many legitimate reasons, but once the percentage of conservatives drops below a certain threshhold (5%?), a tribal moral community forms, and it is only at that point that discrimination becomes a serious force, which discourages the occasional conservative (or liberal Christian, or just centrist non-liberal) who would like to join the field.

I think he's probably correct about this. And I do agree that some amount of ideological discrimination exists, especially in the humanities and social sciences. My point is that ideological discrimination is probably a small factor in the tiny amount of Republican-supporting academics. But that doesn't mean we should ignore it completely.