Gay Marriage and Gay Rights in general is the Civil Rights movement of modern times, just as skin color segregation was the same, years and years back. As time goes on, the narrow-minded, stubborn individuals who can't accept people's choices in this way will change their mind, or die off, leaving the newer generations who are usually far more open-minded, to accept and even promote people's rights to do what they want :3 Blunt, but true.

Yes, I know. It still bothers me. I really hope I won't be so narrow minded when I'm a part of the older generations.

You won't be. How people grow up determines how they'll be when they're older. If you're open-minded now, you're unlikely to lose that open-minded mindset. Narrow-minded people are narrow-minded because things like open, accepted homosexuality just wasn't talked about when they were young, because it was taboo. It's, literally, a societal generation thing.

The modern day of social media, internet, and instant-communication has lead to a more open-minded and understanding generation as a whole.

Back in the day, people were opposed to things much more, as they were only offered a small amount of beliefs that they were (essentially) forced to follow. 

Nowadays, debates, reasoning, and multiple perspectives are offered to people at a younger age, thus making them, again, more open-minded.

The current state of America (and a lot of the world) is in between phases. The majority of the people are still stuck in the traditional, stubborn, old mindsets. The newer generations develop at an exponentially increasing rate, just as most other aspects of humanity are, in general. The amount society and humanity has come (both socially and in other ways) in the course of the past 15 years far exceeds how much it developed over a period of 100 years, say, back in the 1700's.

That's why it seems like there's this huge split, in today's world, when regarding things such as this. 

gay marriage is legal.  Gay people can walk into a church and get married if the church wants to marry them.

Oh?  It's the free stuff and benefits not being given to them that would be funded by the tax payers that you want?  Well, no.  And while we're at it those benefits provided to straight people by stealing money from everyone else through taxes should be abolished also.

And by the way, separation of church and state does not mean that the state can not be influenced by religion.  That is such an absurd misconception.  the way this country is designed is whatever the 51% wants goes as long as they can make it through all the hoops the founding fathers put in place.

"The problem arises when these religious beliefs interfere with our supposedly secular government."

Stats to begin with:

In the US An estimated 3.5% of adults in the United States identify as  lesbian, gay, or bisexual andan estimated0.3% of adults are transgender.

(http://williamsinstitute.law.ucla.edu/wp-content/uploads/Gates-How-Many-People-LGBT-Apr-2011.pdf)

In the us 77% identify as Christian.

(http://www.gallup.com/poll/159548/identify-christian.aspx)

The government are elected to represent the people. If you presume that 1 in every 10 Christians in America don't support Gay marriage then that's 7.7% of the population against 3.7% LGBT/trans-gender. So buy these stats theoretically its public opinion for it to be illegal?

In any case:

I would be careful, in the end religious issues will spill over then the elected are supposed to represent the views of the people electing them.

The split on Gay Marriage is not as simple as you have stated.