I must begin by saying I do not want to sound like universities are anti-Christian, while there is some bias, which I will discuss, there is as much misinformation about universities. This idea began in the 1800’s when there was a growing trend toward rejecting religion, however, what I think was truer of universities at the time was they were seeking to have a more detailed understanding of religions and naturally subjected faiths to academic scrutiny. I have met some level of resistance in my own life from people who want me to “simply accept what the Bible says”. What these individuals usually mean is to skim the surface of faith and make that my whole faith. In some ways it is not that academics reject faith it is that they pose deeper questions which can tear apart the shallow faith of others who do not look so deeply into these fields. For many academics this result is not intentional they simply want people to take their faith seriously.
That being said, there is a notable bias among academics against any religion, though the bias is stronger against some religions. I believe the basis for this bias is pride; academics train for years to become experts in their field and this type of training leads to a pride of knowledge. These experts are very good at scrutinizing evidence and forming working models of the world. This critical mindset leads them to look down on others who do not look critically into issues (like religious books or beliefs). A great example of this is in Richard Dawkins The God Delusion; he talks about Christian scientists like Francis Collins (the head of the Human Genome Project, NIH Director etc.) and is perplexed at how these otherwise critical scientists could allow themselves to simply accept these ancient beliefs. This is an intellectual bias which says, “modern is best and the ancients were ignorant unintelligent people.” As I read that book I keep thinking that Dawkins really didn’t understand Christian belief at all his portrayal of Christianity was so shallow and off-base it made him look silly. At part of the reason for that is he has seen the dumbed down Christianity of Hollywood and other culture wars and assumed that is what Christianity is , rather than looking at the deepest levels of the faith and judging by those. Most Americans would say that ancient Greek mythology represents an almost laughable ignorance in the ancient world, these scholars are simply extending that bias to include the Bible and its explanation of the world.
Christians have not helped this issue either, many Christians remain ignorant of the Bible or at best live in an overly simplistic bubble isolating themselves from deep examination of the Scriptures. I believe this is out of fear of being wrong. This isolation perpetuates misconceptions and makes the Church look unintelligent which will never be appealing to a world (like academia) which thrives (at least in principle) on intelligence. But I think part of the answer is this God is easily dismissed, easily ignored, and I think that is intentional. God wants to be subtle because God realizes how easily overwhelmed we can be and so it is easy to overlook the divine in this world. And scholars who spend all of their time scrutinizing this world can easily miss the divine and look down on people who see God. It is not that the person is ignorant of natural workings when they see God, it is that the academic is ignorant of God when they fail to see anything but natural explanations.
In a nutshell the bias of universities against religion is because of a healthy skepticism which leads to pride and an unhealthy skepticism combined with ignorant Christians who do not want to grow.
For more information see the following:
John Polkinghorne & Nicholas Beale Questions of truth
John Polkinghorne Belief in God in an Age of Science
Francis Collins The Language of God: A Scientist Presents Evidence for Belief