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No relationship, with parents or otherwise, is worth having if a person doesn't accept you for who you are. If you want that acceptance, then you will have to shout who you are in a loud enough voice that everyone you associate with knows about it. (Get some atheist T-shirts and bumper stickers if necessary) You will lose some friends and gain new ones. This process may be difficult, but pretending to be someone you're not is even worse. Get right with yourself, and you will solve the ethical problem that caused you to lie on your application.
Come out! And transfer out of that brainwash-mill you're attending--right away.
Some people prefer that everything be smooth and nice and non-confrontational. That we get along nicely with everyone, no matter what their ideas. But ideas have implications--strong ones. They shape a person's every act. When they are incoherent or hidebound by unsupportable traditions (as we find with most organized religions), they can cause otherwise good people to justify horrendous acts. They make people untrustworthy and unpredictable. God can tell them to do anything, and then God can change his mind.
The bad ideas of religion can also affect your education and modes of thought in subtle and not-so-subtle ways.
You're already way ahead of most people, in that you have philosophically rejected religion. Now claim the prize and fully embrace who you are. I was raised religious and I became a minister when I was 23. I spent precious years of my youth professing one thing and believing another. (Though I kind of made myself believe it for a while.)
I had doubts from the time I was maybe 13, I waited until I was 30 to leave the church, and several more years before I fully came out as an atheist. It was a waste of precious time. Do it now. You'll be glad you did.