How does keeping Fundamentalist influence out of the Government infringe upon freedom of religion?

Last I checked, Freedom of Religion ensures one to have the right to practice their own religion as they please without the government meddling, albeit your not hurting anyone. Yet Im pretty sure Fundamentalists are not losing any rights if matters that fundamentalists find wrong are not outlawed. And we know freedom of religion should not give one the right to tread on anothers rights.