Religious opponents of same-sex marriage worry that if (probably when) same-sex marriage or civil unions become legal, people like them will be prosecuted. This is not far-fetched. "Hate speech" laws could easily be used to prosecute speech, even sermons against gay unions, as they have already been abroad. Religious charities have already stopped placing all adoptions because the state threatened them for not placing children with homosexual couples.
The first few states to legalize same-sex marriage did so by court decisions. These are blunt instruments. They invalidated existing laws without doing the necessary political work to deal with the unintended consequences of the court decision. Now, though, several states are taking the better path, making this major political change through the proper political means, the legislature. When states debate laws, they hear from all kinds of people who would be affected. The states that have passed same-sex marriage laws were able to put in protections for religious groups. Legislative debate, and laws that actually make it through the political process, are better protection for everyone.