Are these institutions Private or Public?  If they are public, I agree that students should have the legal right to carry on campus.  If they are private institutions I would make the argument that the private institution has the legal right to choose if they will allow students to carry on campus or not.

I'd bet it actually is about guns to some degree.

I don't know the ins and outs of free speech requirements at different kinds of colleges and universities, but at my university it was always a hotbed of controversy. Umpteen million political, religious, and lifestyle groups always wanted to spread their message any way they wanted. There was a lot of pushing the envelope in the area of civility. The university allowed almost any group and any message, but they were expected to restrict their activities in certain ways so as not harrass or interfere with the day-to-day business of the university.

Although it may be irrational and not entirely fair toward the pro-gun groups, guns on campus make a lot of people afraid. And this is where free speech starts to bleed over into crying fire in the theater. I would think there's a wiser way to approach this discussion than frightening people. In a similar vein, I wouldn't want an anti-abortionist chasing me down the sidewalk shaking a bloody, rubber fetus in my face.