How can the US gov't have laws against something that is based on religion?

I'm not entirely sure I worded that correctly but what I'm getting at is this. How can the US gov't make it illegal for homosexuals to get married? If it weren't for religion there wouldn't be any reason for there to be any laws against homosexuality. Our gov't is supposed to be separate from religion, yet it is clearly not. Isn't having laws against homosexuality against the Constitution where the founder fathers decreed that there be a separation of church and state? I mean obviously people are allowed their opinions about homosexuality no matter their religious views but that shouldn't be allowed to be carried over into law. I just think the world would be so much better without religion.