Rick Hills claims that many academics have an "irrational fear of, or intense discomfort around, theist and, in particular, Christian, beliefs," which he labels "theophobia." I don't doubt that there are some academics who hold such views. But I think that most seeming academic hostility to religion is actually hostility to the association between religiosity and conservatism in current American politics. Academics are overwhelmingly left-liberal and some of them are not particularly tolerant of right of center political views, whether religiously motivated or not.
Certainly, most liberal academics have no objection to religiosity when it is associated with political causes they support. Many liberal and leftist academics are sympathetic to "liberation theology" and other efforts to associate religion with left of center causes. Martin Luther King is a hero to most liberal academics even though he was a Christian minister. Barack Obama's open religiosity doesn't seem to have hurt his image among academics either. The late Robert Drinan was a prominent left-wing law professor and also an ordained Catholic priest. His religion doesn't seem to have attracted any significant academic hostility.
On the other side of the ledger, I know of a considerable number of conservative and libertarian academics - myself included - who are atheists or agnostics. As far as I can tell, the hostility that we sometimes encounter in the academic world because of our political views is not significantly reduced by our lack of religiosity.
While there are probably some academics who are hostile to religion as such independent of its perceived association with political conservatism, this is a relatively minor phenomenon. Certainly, such generalized "theophobia" among academics is far less common than is generalized hostility to atheism in the general public. For example, as I discussed in this article, some 51% of the general public believe that "[i]t is necessary to believe in God in order to be moral and have good values" and 50% would refuse to vote for a "well-qualifed" candidate for president nominated by their party if he were an atheist. By contrast, I doubt that more than a tiny fraction of academics believe that you have to be an atheist or agnostic to "be moral" or would refuse to vote for a presidential candidate of their party merely because he was a religious believer. Indeed, the vast majority of academics are going to support Obama this year, apparently unconcerned by his religious beliefs. Admittedly, I don't have systematic survey data on academics' attitudes on these points and so would welcome correction from anyone who does have such data. But these are my impressions on the basis of many years spent in the academic world, and acquaintance with a wide range of left of center academics.