I appreciate Jennesque's advice. There's something to be said for getting along, even if you have to fake it.
But as Shakespeare said, ..."To thine own self be true."
It's really nobody's business what you believe, only how you behave. Learn to change the subject or insist on others' respecting your privacy. Get mysterious, they love that. Don't discuss it at all, with anyone.
Read Richard Dawkins' The God Illusion. or anything by him. Find an athiest discussion forum that you like, people with your point of view, for encouragement and solace.
Hang in until you're eighteen. Then show them your back.
I totally agree that you should be true to yourself, but not everyone wants to stick out like a sore thumb, and that's something that may happen to an atheist at a Christian school. Personally, I'm a very introverted person. I like to keep to myself for the most part, and I don't like people gossiping about me. I don't care what they think, but I also did not want the entirety of my 7th and later 8th grade class, teachers, pastors, classmates parents, etc talking about how I lived my life. I don't like to call attention to myself. I'm not sure if the OP is like that at all, but that is why I chose what I felt was the most subtle route I had to show I wasn't a true believer, because the people at my school were always in everyone else's business. It's only because they care about what they believe to be the welfare of your soul.. they're not doing it to be cruel.
It might be hard to lie to yourself, but sometimes being honest about something, at least in this case, can be more difficult. Being young, it might be best to just go with the flow as best you can tolerate it, unless you're an adult and free to live your life as you please. Throughout middle school and high school I always told myself that nothing really mattered except my grades and what I learned. The only people I still see from that time period are the only ones that matter.