It's best to keep Gov't as religion-neutral possible (in my opinion). If you fail to do this, you are opening the door to authoritarianism and a government that will eventually want to control even the most private areas of our life, including bedroom practices, marriage practices, etc.
I think that's exactly what our Founding Fathers were trying to do. Their experience was the single state church of Great Britain - The Church of England - and the onus it placed on the citizenry. It appears their belief was that everyone should be able to practice whatever religion they wished to without government interference.
Sadly, the left has taken these meanings to impose the exact same censorship they were trying to negate.