The founding fathers understood that if government has the power to grant us rights it is also within the power of government to remove them. As a matter of law our constitution is written in a manner consistant with the idea that our rights are granted by God, that government has no power to remove them. They thought they had been quite clever in doing this but the states disagreed. You must understand these were people who had been forced to be members of the Church of England all their lives. The fear was that government could create a state church and rule the people through it, sidestepping the protections the founding fathers had created. In order to preserve inalienable rights the two clauses were composed. The establishment clause meant exactly what it says, CONGRESS shall make no law...and was was written with the intent of separating the federal government from the church. The free exercise clause goes further in preventing government from establishing a state church by reserving that power for the states, as it prevented the government from abolishing the state run churches that existed at that time. The state run churches were also considered oppressive and were abolished by the people, and for many years matters of religion were in the hand of the people, with no interference from government at either the federal or state level.
The religious protection of our inalienable rights provided by the first amendment was eroded when the federal courts assumed they had the power to decide matters of religion, an action that stripped us of that same power. Now matters of religion are decided by federal courts, a branch of the federal government. Since the first amendment was written expressly to prohibit the federal government from being involved with religion, that power having been assumed by the federal courts signals the end of the protection that amendment provided towards the concept of inalienable rights. As the courts busily abolish any and all legal references to God our rights become more and more defendant on the willingness of government to allow them. Once this is completed the U.S. Constitution is fairly worthless, and sadly enough, it already seems pretty much a done deal.