Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereofSounds pretty straight-forward doesn't it? It's my religion, you can't tell me how to express it. You can't make me pay for contraception insurance coverage for my employees, even if they're not of my faith.
Reality is more nuanced though. Mitt Romney can only marry one wife, even though Joseph Smith said otherwise. If I were a worshiper of Satan, any human sacrifice would be considered murder. Mohammed Atta, if he'd lived, would not have received a free pass even though the hijacking was an expression of his perversion of Islam. All these things have something in common: they are religious practices that harm other people. Refusing to include contraception coverage in your insurance coverage for your employees harms those employees. You, as an individual, are free to not use contraception, but the government is within its rights to insist that you cover contraception in your insurance package, just as you cover erectile dysfunction treatments. QED.