I've never eaten at Chik Fil A. Funny, it was their Christian values that kept me from doing so, but at the same time, I didn't boycott them. Actually, I wanted to do business with them, but the only times I was near one of their restaurants, they were closed because it was Sunday. Funny thing, at that time, they handled Christianity in a non-political manner: Their signs said they were closed to allow their employees to attend religious services. Actually, I found that good PR: no political statement, but a concern for their employees. I'd worked for a restaurant that had a similar policy, although it wasn't a chain or franchise: privately owned. The owner once told me that it didn't bother him because if he had to rely on the business of one day of the week to keep his doors open, then he was in the wrong business. Nothing political there, although he finally did start opening on Sundays back in the 80's, he hated to do so.
Chik Fil A could have had my goodwill and maybe my business, had they not chosen to make their Christianity a political talking point. The minute they did that, they lost all credibility. They are a business, not a church. If they were a church, they could have held services at their restaurants every Sunday. It's a two edged sword: they are betting that they can get enough Christians to be offended by those that don't share their values.
IIRC, the school where the concern is being raised is a state university, funded, in part, by tax dollars. This blurs the line of the government not establishing or endorsing a religion. The students have their right to protest (Read the First Amendment carefully) and while it may not be in tune with your beliefs, they still have that right.
But then, I've been known to offend people by slamming my door in the faces of Jehovah's Witnesses.