Metaphysics and mysticism include spiritual matters always tied with physically manifested events, in deist, "secular" terms that people may know as pantheistic, in that the deity is understood to be in all things, everywhere, and all-knowing.  God is in all of Nature.  Thus, analogous to understanding that education does not conflict with one's own belief system, one's individual understanding of universal laws also is in no conflict with religious tenets.   In fact, an understanding of universal laws and principles rather than negating, further enhances an understanding and practice of any religion. 

Individuals who believed in freedom of religion and the separation of church and state, understood why people should have freedom of thought and expression in matters of conscience.

Some founding fathers are known also as the first American Masons.  Benjamin Franklin was the first American Masonic Grand Master.  George Washington was a Masonic Lodge Master.   Thomas Jefferson, too, was a Mason, judging from a note he wrote in his own calendar of a Masonic event where he was to be present.  Heironimus wrote that there was a strong network of Masons involved in actually fighting the war of the American Revolution, many who surrounded General George Washington and contributed a great strength when times were extremely difficult, making it possible to fight, unswerving, to the end victory of independence.

Well known historians aside from Rosicrucians themselves, have written that the early Masons in America were actually led or inspired by those who were also the same Rosicrucians involved in European political and religious movements.

American Rosicrucian adepts in particular were few in number by comparison with the more public, culturally networked Masonic Order.  As indicated earlier in the discussion of Kelpius and the subsequent Zionitic brethren, Rosicrucian replacements were requested from Europe; neophytes were not inducted in America at that time.  Rosicrucians even in the 18th Century were much more secret than Masons about their fraternal work, as in Europe.  They were often referred to as "unknown" philosophers, many doing what they did very subtlely or behind the scenes while intending that others instead be credited with their authorships or be written down in history for that which they themselves had initiated or generated. 

Whether Rosicrucian or Mason or both, as many Early American leaders were, in addition to participating in their own respective religious affiliations, the influence of the "deist philosophy" in great Early American thinkers is clear in history. 

The founding fathers included men of science as well as men of theology, and most assuredly, they were well educated men who joined in leading others in making a most significant turn in world history.