It is so antithetical to their way of doing things, and forces you into a state of mind they hate. It gets you out of whatever bubble you live in. You're expected to be an adult, which is the exact opposite of what the society wants from you.
In my English 101 class we have watched R rated movies, talked about religion, learned how to recognize and dissect propoganda and my professor openly states that his goal is to challenge our prejudices and ways of thinking. Plus I have group projects that require me to *gasp* meet with people with different ideas and backgrounds in a semi-recreational manner.
My biology class openly teaches evolution and all the evidence for it, and much to my surprise even though I am in the bible belt and alot of my classmate are people returning to college later in life, most of the students accept evolution as a fact after class. In all of my classes, debate and questions are encouraged, my professors make themselves available and are open to answer any questions personally, and don't just refer you to the text book.
My professors openly do not give absolute reverence to the bible. My english teacher stated that in any research bible, the bible or other holy books are not a citable source. If you're in a philosophy or religion class, then in may be acceptable depending on context, but other wise your holy book is not a reference. This mind set is so vastly different from anything in any kingdom hall. He's not berating the bible, or saying it's a lie. He just wants to to learn to face the world objectively outside of your personal interpretation of your holy book of choice. That is a radically different paradigm that would scare the society's socks off.
If I was a witness that secretly harbored doubts, (like I was five years ago), it would only take a semester or two to make me question my entire system of beliefs and examine it with the tools I had been given. The society hates college because they know that an educated person will almost certainly reject their absolute authority.