The Alliance Defense Fund has written a letter to officials at the University of Wisconsin-Madison and UW-Superior urging them not to abridge the speech and associational rights of student religious groups. At issue is the conflict between university non-discrimination policies and the fidelity to their missions of groups like the Knights of Columbus and the Intervarsity Christian Fellowship.
The Inside Higher Ed piece suggests that the only issue is access to funding, not recognition (and access to university facilities) per se.
I should also note that the fact that some groups prosper (by their lights) while conforming to the universitys non-discrimination policy says nothing about whether other groups ought to be required to do so. Different groups ought to be permitted to be different. Denying money to those who would be different does approach the kind of viewpoint discrimination against the Court ruled in Rosenberger.