I felt like my experience was quite a bit different (graduated '08, so I'm not sure wen you were there). I think this is te general perception of BYU and a lot of the departments, in my opinion, had a chip on their shoulder about it and wanted to prove otherwise. This was, from what I saw, prevalent through the hard sciences and especially within social sciences (particularly psychology). I took a course titled something similar to 'Psyhology and LDS Perspectives,' expecting it to be viewing psychology through the lens of the gospel. Surprisingly, it was almost exclusively viewing the gospel through the lens of psychology. This was my first semester there (spent 1.5 years there) and then no longer was surprised when BYU continued to be conservative and hard line in reputation only.
My frame of reference largely refers to religious issues. Outside of religion classes, I can't recall any professors who overtly inserted religion into the classroom instruction in areas not related to religious belief. BYU (unlike some other Christian universities) openly teches and supports evolution and appears to be to adhere rigorously to scientific process. That said, IF you find yourself reaching conclusions about religious truths different from LDS teachings, you must tread very very carefully. As someone who went through this experience, and who know other people who have gone through this experience, I know first hand just how intolerant BYU is institutionally to those who seriously question or lose their belief in Mormonism. This includes a good friend (and this is one of many examples I am aware of, and I only see the tip of the iceberg), former staff member there who was a 'liberal' Mormon but active and committed to the Church, who having said one intemperate thing to a student who he though was also a bit more liberal in her beliefs, and whose father happened to be among LDS hierarchy, was summarily run out of the school and terminated within a couple weeks time through a process that can only be described as inquisitorial in nature. While BYU will allow some divergence from orthodoxy, this is true only to a point. Once you cross a very ill defined boundary (which varies depending on who is in authority and how pious he happens to be), you become a threat and are treated as such.
To understand this, it helps to realize what BYU's primary mission is: to create a pipeline of dedicated, faithful, loyal, tithe paying members who form an important core of the Church's membership (at least North American based) and leadership. Institutionally, BYU is dedicated and active in seeking to root out perceived subversives who threaten this mission.
Years ago BYU (LDS Church) commissioned a panel study (longitudinal study of the same cohort of students) looking at students who were marginal acceptances (just above cutoff line for admission) and marginal rejections (just below cut off line). After tracking these students for several years, the study found that students admitted to BYU were significantly more likely to be active & contributing members to the LDS Church than those not admitted. The study concluded that the primary causal factor was the intense socialization process that is part of the BYU experience. (This was an internal study and not published.)
Understanding the implications of this study and BYU's mission, it makes perfect sense why BYU tends not to be tolerant toward perceived apostasy or perceived apostates (this makes perfect sense to me and in one respect I don't blame them), although this vigilance serves also to create an environment in which one is open about 'subversive' beliefs or opinions at his/her peril.