When our forefathers founded this country, they believed in God. And so the Constitution prohibited the establishment of a state religion or any laws prohibiting the free exercise thereof. It was not their intent to rule God out of public life, but to avoid sectarian religion gaining control of the government and dictating forms of worship.
They recognized that any government must be founded on some moral authority, and the moral authority they recognized was God. The founding of our civil religion was on God. But the founding fathers knew how intolerant religion could be, so they included these protections in our founding document.