Separation of church and state means that a religion cannot impose its beliefs on non-adherents to that religion.
A Chriustian Scientist might say that providing blood-transfusions violates his or her conscience. Should a person bleeding from a femoral artery be denied a blood transfusion because it is against the conscience of some Christian Scientists? Of course not.
Mandated health-insurance coverage for contraception is not mandated contraception useage. Nobody – Catholic or non-Catholic – is forced to practice contraception. Just like blood-transfusions.
If we are indeed a free country, a person following one’s conscience does not include his right to control the lives of others unless they are infringing on his liberty.