"Government is instituted to protect property of every sort. Conscience is the most sacred of all property." - James Madison
When asked what the most important freedom is that our Constitution protects most Christians would say it is the freedom of religion. However, in reality it is the freedom of conscience. Conscience is what God wants you to do. Our Founders were more concerned that the government not encroach upon one's conscience and force people to think the way a tyrant would want them to think and participate in its sin. Today we refer to tyrannical action on the part of the government as political correctness. The courts have abandoned the freedom of conscience as they try and force Christians to go against their conscience and participate in the sins rampant within our nation.
The biblical justification for the rights of conscience are found in 1 Corinthians 8: 12, 10: 27 - 29, Ephesians 4: 2, Colossians 3: 13 and Romans 14: 3, 15: 7. Our Founders were very aware of the tendency of the government to override one's conscience after their experiences with the English government and the tyranny of King George. They wanted to insure that the newly formed American republic would not force a citizen to go against their conscience and participate in the sins of the nation. As time progressed we lost the connection between the importance of protecting the right of conscience. With time our thinking on the role of government and its relation to protecting the right of conscience shifted to the point where we now believe the role of government is to protect freedom of religion. This is a big shift and dilution from the Founders original emphasis on the protection of the right of conscience.
In the following video clip David Barton gives an excellent presentation on this topic.