No religious organization is being forced to recognize same-sex marriage. No religious organization will be required to endorse same-sex marriage. The case is solely concerned with the question of whether the state of California in its capacity as a state of the United States has grounds to refuse such recognition. And, under the 14th Amendment, it does not. That's the whole thing.
As to college housing and other situations, the real question is whether such colleges accept government funding. That puts you in the same situation as accepting any funding: the entity providing the funds has the right to attach conditions, and you have the right to accept or refuse (and if you refuse, you don't get the money). And the US government and state governments are constitutionally barred from providing funding to any entity which engages in certain types of discrimination, so that's the condition attached to the funding.
As to college housing and other situations, the real question is whether such colleges accept government funding. That puts you in the same situation as accepting any funding: the entity providing the funds has the right to attach conditions, and you have the right to accept or refuse (and if you refuse, you don't get the money). And the US government and state governments are constitutionally barred from providing funding to any entity which engages in certain types of discrimination, so that's the condition attached to the funding.