Because the Bill of Rights provides for religious freedom, there must indeed be a separation of church and state… to a certain extent. Meaning, any public institution should not force any individual to practice or adhere to any specifically religious item; however, the same institutions should also not prohibit any individual from doing the same. For example, an atheist child should not have to pledge “one nation under God”; but a Christian child should be able to wear a Christmas sweater to school.
It also comes down to basic values as well. If a courthouse has a biblical quote on a wall, there is no harm in it as long as it is about a generally good value, such as one that the law already supports. For example, while the Ten Commandments are Judeo-Christian, the commandment against killing supports the laws against murder.