It's been about 20 years so I don't recall specific things that were said but I was attending there around the time the church was purchasing the Main Street area east of the temple. Lots of negative opinions were expressed about the church and there involvement in purchasing the land. Sorry, I don't recall anything specific. I had a Utah History professor that would make little jabs about the church and church history frequently in lessons. I would often come home and vent to my wife about it. I remember a teacher in a multi-cultural class talking about the church in not so positive ways but again it's been too many years to remember specifics.
So in total I recall three professors saying things on a regular or somewhat regular basis. Over the course of two semesters and one or two summer classes I felt like that was a bit much especially when other kids start to comment as well it just turns into a really negative atmosphere that I didn't want to be a part of. I know there are a lot of great people there (students and faculty) but my time there left a bad taste in my mouth.
I am glad that you and others have had positive experiences at the U. I know a lot of people that really enjoyed it there.