My engineering classes had very few members, but no one cared about religion. We didn't have class discussions about social issues or anything like that. Didn't come up once in 5 years.
My law classes, on the other hand, you definitely noticed the anti-Mormon sentiment. Rarely (maybe once) from teachers, but a lot from classmates. Going to protest at the Main Street plaza was something people did for fun. Weird stuff.
I never felt though that the administration was anti-Mormon. Mostly just the students.