Thomas Berg notes some of the concerns same-sex marriage presents to religious liberty beyond mere disputes about gay and lesbian couples being married in churches:
Antidiscrimination and public-accommodation laws in California and other states could force many religious non-profits to give direct assistance to marriages or ceremonies that violate their tenets. Catholic Charities ceased providing adoptions in Massachusetts and, to a large extent, San Francisco because it faced being compelled to place children in same-sex households. A religious college that provides married-student housing might violate state law if it refused to house same-sex married couples. These groups can face civil liability or the loss of generally available government benefits such as tax exemptions or licenses.
Marriage ceremonies also affect small businesses "“ wedding planners, caterers "“ in which individuals directly lend their personal skills to facilitate marriages. An Albuquerque, New Mexico, wedding photographer had to pay more than $6600 in legal fees for declining to photograph a same-sex commitment ceremony. In short, religious liberty is a context where gay marriage may affect others directly.
Marriage equality is happening. Outside of the National Organization for Marriage folks, there aren't many who deny its inevitability. So the question for conservatives must shift from "will we allow same-sex marriage?" to "how do we accomodate this societal shift?" Doing our darndest to protect religious liberty in a very broad sense is a start, and a most important one at that.