The United States is premised on the separation of church and state. But over time, what that separation means has changed.  The founding fathers wanted to ensure that people were free to practice whatever religion they wanted. Moreover, they wanted to ensure that the government did not establish any official religion. You will regularly hear the ACLU refer to the "establishment clause" of the US constitution as the basis for their various lawsuits against states.

It's a sticky situation because for such a long while, the percentage of Americans who were Christians were so high that religious concepts made their way into government policy. This wasn't intentional in most cases. If you're a true believer many things that are religious in nature just seem natural, common sense, normal. One such thing is marriage.

In hindsight, it was probably a bad idea for the government to recognize marriage as anything beyond a civil union. But it's easy to understand why this happened. Marriage is such a normal part of human life that how could the government not recognize it?  As an agnostic, it's never bothered me either way. I am comfortable with my beliefs and do not feel threatened by people's religions. In fact, I embrace their beliefs because it helps create a deep tapestry of culture that enriches us all.

I also believe in two social principles: 1) That the traditions of the super-majority should be respected and protected. 2) The rights of the minority should be protected.

I think government should get out of the marriage business entirely. I support the right of any two people to "get married" regardless of sex.  However, the super majority don't think the government should recognize these unions. And by our constitution, that's pretty much that. Marriage isn't a "right". The 10th amendment makes pretty clear that anything not explicitly outlined in the constitution is left to "the people" (in the form of their democratically elected representatives).

That said, gays should have access to civil unions that have the same legal punch as marriage. It may seem like semantics but to millions of Americans, it's not. There is a principle involved here. The same people who argued that the Super Bowl nonsense with Janet Jackson was "no big deal" are likely to not see why people object to gay marriage. The majority of Americans believe in these traditions and they have been with us for literally thousands of years. All around us, however, small minorities seem bent on using the government to infringe on those traditions.  Marriage is a cultural phenomenon, not a religious one. And as long as the majority of Americans practicing it believe it should be between a man and a women exclusively that is what it should be. It's their tradition. Contrary to what some may believe, majorities have rights too.

The government should work to ensure that civil unions have the same legal meaning as marriages. Two consenting adults, regardless of sex, should have the right to form a legal union.  For that matter, I believe that any number of consenting adults should be able to form civil unions (whether you're into "Polyamory" or whatever). But marriage should not be open for redefinition by a small minority of people. And they should not be trying to use the tools of government to hijack it for their own uses.