Marriage is an institution in our world, and to reflect that need for the institution, the government offered certain legal rights to married couples. It was completely sensible. And the simplest way to do this was to just have the state recognize marriages that were already happening everywhere, and all was fine. The problem is that states were recognizing a religious institution, and over time, that became muddled. Now, it is completely reasonable for the government to recognize gay marriages in that same spirit. However, suddenly there's this awkward relationship between the church institution and the state institution that was completely harmless until people started acknowledging the existence of gay people. And some powerful christian lobbies start to feel like the institutions are one in the same. Truth be told, there should be a civil marriage and a religious marriage, and the church can call marriage whatever the hell they want. Even let churches keep the term marriage, and call all state sanctioned marriages civil unions, but it seems like that ship has sailed.
Two things though. One, Gay Marriage will be universal in America. It's inevitable, and already exists in some of the better states. People who say otherwise are deluding themselves. Two, there are churches fine with homosexuality. Hell, the church I grew up said that they would marry gay couples before Gay Marriage was legal in ANY state.