Well, let me try to clarify.
I believe that the government should have no role in the affairs of religious organizations, with the exception of the protection of minors or other civil rights violations. Neither should the government fund said organizations in any way, nor show preference toward any religion. I believe the United States is a secular republic, not a Christian nation. We are a nation made up predominately of one variety or another of Christians with other beliefs present, but none have the right to use the power of the state to impose their will on others, nor to levy taxes to support their religion. President Kennedy said it well:
"I believe in an America where the separation of church and state is absolute--where no Catholic prelate would tell the President (should he be Catholic) how to act, and no Protestant minister would tell his parishioners for whom to vote--where no church or church school is granted any public funds or political preference--and where no man is denied public office merely because his religion differs from the President who might appoint him or the people who might elect him."
Does that help?