Marriage vs. Civil Union

Help me out here, I think I may be confused.

Is marriage a religious act or not? Because I keep hearing how marriage is religious and that gays shouldn't marry because it's against Christianity and blah blah blah. Okay fine. Let's accept, for the sake of argument, that marriage is religious and that homosexual marriages are banned based on Christian doctrine. Hell, let's say that every single religion out there that has in it's arsenal some prohibition against gays marrying. Fine. You can't get married in the eyes of the church!

Marriage is a religious act.

So here's where I am confused. The United States of America recognizes marriages as de facto evidence contractual unions between two individuals. When those two people are a male and a female, we call that a "marriage." Now some states allow two people of the same sex to join in a contractual union but we don't call it a "marriage" because they can't be married since it's against religious doctrine. We call these "civil unions." Am I right so far?

Here is where I am utterly confused. Why does the United States government recognize marriages AT ALL? I mean, I'm okay with a wedding being evidence of the intent of two people to join not only in a spiritual union ("marriage") but also in a contractual union ("civil union"). But why do we use religion to determine why people should and should not be united? Am I confused about the fact that there is a separation between church and state here?

So check it! I don't believe that people should be "married" in the eyes of the government. Not straights, not gays. It's all Civil Unions. Whether or not you are "married" is between you and your church. And we should ALL be allowed to join into contractual unions with whomever we choose.

Besides, if anyone should not be allowed to marry it should be atheists.