Dep Dog,
Humans are in the habit of presuming their beliefs are the 'troof' or the only way. Humans also have the habit of putting themselves above others who are not of the same opinion
A example of this would be the Danbury Baptist, the Baptist at the time were a minority (read cult). The state of Connecticut considered religious freedom not as a right but as a privilege. Petitioning Thomas Jefferson for relief this slight led him to write his Wall of Separation Letter. As a thank you for his actions this subversive little sect sent him a 1200+ lbs hunk of cheese, hence was born the phrase to be a or the 'big cheese' for someone of importance.
Another example is the Inquisition, the Roman Catholic Church managed to be greater in importance, influence and power then Kings.
If there was not separation how long do you think it would take the religious right to take control over most of the government. In his book "What's the Matter with Kansas?: How Conservatives Won the Heart of America" Thomas Frank says that the Republican Party had managed to get people to vote their values over self-interest. Need proof count all the red states versus blue states. It wouldn't take many decades for areas of the South to be divided into Catholic, Methodist, and Southern Baptist etc. Constitutions can be amended and laws changed.
Actually come to think of it just imagine if the WBTS was in charge of everything, remember the nit-picking, hounding and tattling.......without separation it could happen.
Humans just aren't that compassionate, sad but true.
Guess it is like speed limits, while being an impediment of freedom (and the need, the need for speed), it affords protection and safety for the general public.