Daniel Drezner provides numerous links to this recent heated discussion in the blogosphere. Bruce Bartlett summarizes the data on bias in academia. My perspective is closest to that of Jacob Levy, who offers the following advice to budding academic conservatives and libertarians:
[I will tell you] The same thing I tell everyone else. If you love it, do it; and do it well, and honestly, and in good faith. Don’t do it to advance a partisan mission; you won’t get away with it. But if you want to do it for its own sake, you should– and enjoy it.