I think one of the biggest problem with our culture is the idea that there is such thing as true religion, false religion, and neutral philosophy.
The Bible tells us that there are only two humanities on the planet, and that each has its allegiance to either God or the devil. All of their concepts, desires, devotion, etc. find their worship to one or the other.
Of course, since Christians live in the "already, not yet" limbo of their sanctification, they can be seen as having both allegiances at times. The world, however, is enslaved to the one. It has no allegiance to God, but only to Self, which is the religion of the devil, as it emulates his self-appointed deification.
But what this means is that no institution based in secularism, our version of the religion of the Self, can be seen as neutral. Yet, this is where most evangelicals get into trouble. Once you believe that secular findings concerning questions that support or undermine God's Word are neutral, you're going to conclude that the Bible must be wrong, since these findings are purely unmotivated by a culture's religious devotion.
Then, one can paint those who do not accept those findings as legitimate as simply being dishonest and anti-intellectual. This attitude, in return, breeds unbelief in the Scripture, as a stance of belief in what undermines the Scripture cannot stand with a belief in the Scripture without radically altering what it means to believe in the Scripture, radically altering the Scripture, and truly being dishonest with the fact that the secular, Satanic religion of the Self is not compatible with biblical Christianity, precisely because it has been designed to be that way.
The academy, from the time of the Enlightenment on, has been little more than an institution bent on undermining orthodox Christianity and the Bible. It is an apologetic factory for the devil who rules it, as he rules all institutions in the world that are not a part of the kingdom of God.
Hence, there is no neutral ground. There is no academic freedom as opposed to that which is tied to an apologetic of a religious stance. All academic positions argue for a religion. The academy just covers that up by believing and portraying itself to be neutral. But you don't go to universities to learn raw data. You go there to be brainwashed into confusing data and its secular interpretation cannot be divorced, and therefore, the secular interpretation of that data is fact. Anyone who denies it is merely denying facts. Hence, the secular view of reality is gained via a manipulation of a society that gives it the place of a cult leader in a cult, or perhaps, a cultic organization.
My favorite line, often given by the poor manipulated souls who have been thoroughly indoctrinated, is that there is "overwhelming" evidence for some position that undermines the Bible. The reason why I think this is a joke is because, having studied cults and the way that people are sociologically conditioned, every cult would say the exact same thing. There are overwhelming lines of evidence for Mormonism, as long as you are a Mormon scholar. There is overwhelming evidence for the superiority of one race over another, as long as you are a part of a racist cult. There is overwhelming evidence for Scientology, as long as you are a part of that cult. Everyone takes data and interprets it according to his or her worldview and presuppositional stance. That's the way ultimate/necessary beliefs work. You can't interpret reality without a faith stance, and the Bible tells us that one has a faith stance either in one of the many manifestations of the religion of the devil or in the religion of God.
The world's fallen institutions and intellect are the medium for the devil's religion. The Word of God, as it is impressed upon us by the Holy Spirit, is the medium of God's religion. Hence, Jerusalem can use Athens if it is wary of its purpose, but it cannot submit to Athens without giving up the religion of God, since Athens has been designed by the devil to destroy the religion of God. Whatever other things it does to throw humanity of the scent of its true purpose, that is its primary purpose in the world. Secular academia exists for no other purpose than that.
Now, can God not use what is meant for evil for good? Sure, that's what I mean by Jerusalem using Athens; but it becomes a dangerous game when one is not conscience of its purpose. God could use Mormonism to teach Christians, but how many Christians will come out of such an education without being scathed by it? Without in some way thinking that maybe Mormonism is true, or maybe there is a way to reconcile both Mormonism and Christianity together. Certainly, not in a way that preserves Christian orthodoxy, as the religion of the devil can only be compatible with the religion of God if one or the other is distorted.
Some of this comes from the idea that what is fallen in human nature is the heart, but not the head. And much of that stems from misreading the Bible when it talks about the heart. As I have said many times before, "heart" in the Bible, especially in a Semitic context, most often refers to the mind/thoughts of a person. Hence, it is man's mind, and all that comes from it, that is corrupt, distorted, and deceived above all things. It is, thus, from his mind that all evils flow. His intellect is fallen. His academic thoughts are distorted. He cannot see clearly, and his mind works toward the establishment of his religion. It seeks nothing else beyond ensuring that his religious sentiments and lifestyle are true and good and those that contradict it are false and bad (or less true and less good as falsehoods and evils are often presented in our "pluralistic" society).
But what does this mean for an evangelical institution that was based in becoming more intellectually appealing to the world? Evangelicals want academics that are respected by the secular world. Their Bible colleges and seminaries want professors who are educated by secular institutions more than they want professors educated by Bible colleges and seminaries. After the controversy over Peter Enns at Westminster, Carl Trueman made the statement that what we really need to ensure that such things don't happen is professors who are trained with PhD's from the secular academy. Hugh? Dr. Enns has a PhD from Harvard. I would think that anyone with half a mind would link it to the problem, not the solution. But this is precisely the mentality that has shipwrecked evangelicalism, and any orthodoxy that may have thrived within it.
The truth is, we are now living in a secular society that has worked hard to establish its voice as the dominant one by portraying its primary authority, the academy, as a neutral party. It just happens to be a neutral party that undermines the Bible at every turn, but since it's neutral, that just means that the Bible's errors are factual. See how that works? If the Bible were are primary authority, it would mean that the errors of the academy, and its secular religion, are factual. But we have allowed ourselves to be painted into a corner by letting the academy get away with presenting itself as neutral when it comes to religion and Christianity as a faith stance toward a religion. So the devil doesn't need to transform himself into an angel of light in order to deceive the world anymore. He just needs to transform himself into a university professor.