When it comes to the attitude of academics toward religion, I suspect that the truth is probably closer to the view articulated by Rick Hills or Ilya than to Eugene's more charitable view. In particular, what the data (and personal experience) indicate is that the views of academics toward religion is not uniform. In particular, academics have a highly negative view of Evangelical Christians and very little hostility to Jews.
According to a study by the Institute of Jewish and Community Research, 53% of professors have an unfavorable view of Evangelical Christians but only 3% have an unfavorable view of Jews. A summary of the study is here. 33% have unfavorable views of Mormons. Muslims, Atheists, and Catholics all score in double-digits. Who would've thought that 13% of academics have unfavorable views of Catholics?
Now let me say that again--53% of academics have an "unfavorable" view of Evangelical Christians.
It is almost impossible to imagine any identifiable group of Americans today who would hold such a reflexively negative view of other groups of Americans. I can't imagine that any degree of racial bigotry by any group toward any other group would even approximate this degree of bigotry and prejudice. I also have to say that based on my personal observations this finding is completely plausible (note that it was a Jewish affairs organizaiton that conducted the study so one wouldn't expect that it had an axe to grind or was biased toward trying to find evidence of anti-Evangelical sentiment).
So what to make of this? Given that there are a divergence of views toward different subsets of religious groups, this does not seem to me to be consistent with Eugene's thesis that what is going on here is an incomprehension of a religious worldview. It is clear that bigotry toward Evangelicals and Mormons is much deeper than mainline protestants, Buddhists, and Jews. As Ilya suggests, it is likely that many academics simply know no Evangelicals (at least that they are aware of), so this seems to be pure bigotry based on some general prejudice. But I doubt many academics know many Buddhists either, yet very few hold negative perceptions of Buddhists. And I doubt that academics are any more informed about what "weird" views Buddhists hold than Mormons or Evangelicals. All of these views are based primarily on simple prejudice (in the descriptive sense) not on knowledge or experience.
So what about Ilya's thesis that religious bigotry is a proxy for political bigotry? There may be some truth to this. I suspect that Evangelicals and Mormons are generally perceived as political conservative and Jews are perceived as politically liberal. Other views, such as Catholics and Muslims, I suppose fall somewhere in the middle when it comes to such stereotypes. But I don't think this can explain it all either. For instance, I think that most academics are quite tolerant of conservative Jews. I also suspect that academics probably think that it is ok for blacks to be Evangelical or Southern Baptist, even if they dislike white Evangelicals. Ditto for other unusual religious groups, such as the Amish. My opinion on this score is based on hunch, not data, however, so I could be wrong--it may be that academics hate conservative Jews or black Southern Baptists as much as Evangelical Christians, but my instinct tells me that is not the case.
If that is true, then I think the answer must lie somewhere closer to Hills's thesis that what is really going on here is something closer to simple bigotry, hatred, or fear. The source of the bigotry, I suspect, is cultural in nature. Conservative Jews and black Southern Baptists are ok because their religion is seen as an extension of their cultural and ethnic background and academics look at those cultures through a multicultural mindset.
Moreover, I suspect that many academics would say that their negative stereotypes are justified because they have formed a perception that Christians are "hateful" people intent on imposing a theocracy on the United States. So they would say, "My hostility is based on their hostility, so it is fully justified."
Hills's experience reflects a really quite common mindset in my view. And the disbelief that is expressed is not that suggested by Eugene--"Really, how could he believe that?" What the disbelief suggests is, "Really, yet he seems like such a nice guy. How could he hold such [hateful] views?"
Finally, let me stress one final point--what is so surprising to me about all of this is that the views of academics toward Evangelicals and Mormons are likely based purely on stereotypes and ignorance. I doubt that many academics know any Evangelicals (that they are aware of) and few probably know many Mormons, nor do they likely have much but superficial knowledge about the views of many of these people.
A commenter notes that in the population at large there are subgroups who are also viewed unfavorably. Opinion polls show that indeed to be the case to some degree. According to this poll, atheists are viewed negatively by 45% of the population and scientologists by 52%. Evangelical and Fundamentalist Christians are viewed negatively by 23-25% of the population at large.
I have updated the post to reflect this.
Some readers have taken issue with my use of the term "bigotry." I used that term to try to capture the flavor of the response that Rick Hills heard in his friend's remark--"the academic’s irrational fear of, or intense discomfort around, theist and, in particular, Christian, beliefs." The flavor of the remark is that the friend had a negative prejudice against Christians such that he or she was surprised to learn that the person in question was a Christian. This is functionally no different from meeting someone who is inconsistent with one's negative stereotypical prejudices of a racial or ethnic group. I think the correct word to apply to that prejudice is "bigotry," but if there is a different word, then please suggest the correct word. I think that the term must be freighted with greater normative implications than I intended, as I intended it to be used descriptively, not normatively.