While the First Amendment undoubtedly was intended to preclude the government from establishing a national religion as you note, that was hardly the limit of its intended scope. The first Congress debated and rejected just such a narrow provision (“no religion shall be established by law, nor shall the equal rights of conscience be infringed”) and ultimately chose the more broadly phrased prohibition now found in the Amendment. During his presidency, Madison vetoed two bills, neither of which would form a national religion or compel observance of any religion, on the ground that they were contrary to the establishment clause. While some in Congress expressed surprise that the Constitution prohibited Congress from incorporating a church in the town of Alexandria in the District of Columbia or granting land to a church in the Mississippi Territory, Congress upheld both vetoes. Separation of church and state is hardly a new invention of modern courts. In keeping with the Amendment’s terms and legislative history and other evidence, the courts have wisely interpreted it to restrict the government from taking steps that could establish religion de facto as well as de jure. Were the Amendment interpreted merely to preclude government from enacting a statute formally establishing a state church, the intent of the Amendment could easily be circumvented by government doing all sorts of things to promote this or that religion–stopping just short of cutting a ribbon to open its new church.
Except none of this translates into what secular liberals envision it to be today. For instance, there's nothing unconstitutional with lawmakers being against, say, gay marriage because of their religious beliefs. Or, for instance, something like the alcohol laws here in Utah being more stringent because of the predominant religion. Yet, these are the types of things that libs will cry "Separation of church and state" about when there's really no basis. And many liberal judges in the courts have gone beyond what the founders ever intended in order to marginalize religion as much as possible; even rewriting the history of many of the founders themselves to justify it.
