What happened to separation of church and state?

It disturbs me that the very first amendment of the Constitution has been torn apart in our modern day society. For instance on the issue of gay marriage, I don't care if gay people want to get married, they have the right to be as miserable as the rest of us. However for some reason citing the Bible, a text of a religious institution is probable cause to take away the rights from another group of people. Hello! As soon as the bible was the only argument people had for against the institution of gay marriage, that argument should have been thrown right out the window. I've seen religious people trying to get evolution taken out of school as well. They even want to censor other groups. I thought we escaped that religious persecution from Britain, but it's starting all over again, but this time it's working from a societal level into the government rather then the vice versa way with British rule. Why are we letting these boundaries become a blurry figment of our imagination? We need to strengthen the regulations on the separation of church and state. I for one don't want a "good" Christian senator deciding that my children can't learn evolution, dinosaurs, or other religions because he doesn't think it agrees with his god.