Matthew,
Therein lies the rub. It is. The problem is that very few people pay attention. To wit, you are probably one of them. [link|http://www.lawandliberty.org/chur_sta.htm|http://www.lawandlib....org/chur_sta.htm] . To be fair, you are not "American" and didn't have to suffer through American History, but the "separation of church and state" doesn't exist in our Constitution until the US Supreme Court "interpreted" it in in the 1940's. In essence, the "wall of separation" was a construct of Jefferson to keep the Congress and Executive branches of our government from establishing a "state" religion. Until the Fourteenth Amendment, individual states could establish their own religions... This intent was more on the limits of federal power than on the government's stance on religion.

What gets lost in these discussions is that the First Ammendment (the ammendments were the only way the states would buy into forming a federal government - by limiting its power), guarantees the "free exercise thereof". The idea that having the Ten Commandments removed from a public building by citing the "separation clause" most probably has Jefferson spinning like a rotisserie chicken in his grave. This country, a former loyal colony of the British Empire, was sickened by feudal Europe and the Anglican church and wanted somoething different when they broke off from mother England. They still did want Jesus and assumed that Judeo-Christian values (the basis for our government and laws - once removed from Aquinas and Locke) were not only influencing political decisions but were a priori to any legislation...

Now whether or not this is a "good" practice or not is irrelevant in regards to modern governance, but history is history. To accuse people of being uneducated because they do not understand the (simplistically wrong) "common knowledge" that you allude to is a bit naive (at best). As far as "religious intolerance" is concerned, noone is free from that beast.