The increasingly tiresome Judge John E. Jones, who presided over Kitzmiller, the Dover PA "Intelligent Design" case, recently gave the commencement address at his alma mater, Dickinson College. He said the following:
The founders believed that true religion was not something handed down by a church or contained in a Bible, but was to be found through free, rational inquiry.... They possessed a great confidence in an individual's ability to understand the world and its most fundamental laws through the exercise of his or her reason.... This core set of beliefs led the founders, who constantly engaged and questioned things, to secure their idea of religious freedom by barring any alliance between church and state.
That is, of course, a fairly tendentious description of the faith of the Founders. It was true of some of them and not of others. What is interesting about it is that, if Jones means to say that this is the basis of and interpretive model for the "separation of church and state," it itself constitutes the establishment of a certain type of religion. It's not religiously neutral.
The idea that one finds God through one's individual experience is certainly one way of looking at religion. It's associated with modern liberal (not in our political sense) theology that dominated the mainline Protestant denominations for many years.
But another way of looking at religion is that it can only be formed in community and only in relation to the traditions of a particular community. This postliberal view of religion (which I am told is lately triumphant among theologians) says that
"true religion" can only be found in places like the Church or sources of revelation like the Bible. God may be immanent, but we find Her by looking outward and not inward. And by doing it with others. And by taking note of the experiences of those who went before us.
If you assume that "true religion" is only what Jones says it is and then allow that to inform your view of the Establishment Clause (as he did in Kitzmiller), then you've put the weight of goverment firmly in the camp of one - but only one - view of religion.
This tendency to view one's own predilections as objectively true and divinely inspired has been long characteristic of liberal modernist Protestants. George Tyrell once famously demolished the late 19th century liberal "life of Jesus" movement (which then and now generally tries to turn Jesus into George McGovern)by saying that the Christ it finds "looking back through nineteen centuries of Catholic darkness, is only the reflection of a Liberal Protestant face, seen at the bottom of a deep well"
Judge Jones looks for the faith of the founders and finds his own reflection with which he is well pleased.