I know that the case you cite, of Dr. Drake, has been a common one. The religion-builders have so distorted and deformed the doctrines of Jesus, so muffled them in mysticisms, fancies and falsehoods, have caricatured them into forms so monstrous and inconceivable, as to shock reasonable thinkers, to revolt them against the whole, and drive them rashly to pronounce its Founder an impostor. Had there never been a commentator, there never would have been an infidel.... I have little doubt that the whole of our country will soon be rallied to the unity of the Creator, and, I hope, to the pure doctrines of Jesus also (Jefferson, 1854).
American Transcendentalism -- the transcendentalist movement was a group of new ideas in religion, literature, culture and philosophy that emerged in New England in the early to middle 19th century as a generalized protest against the general state of intellectualism and return to orthodoxy often noted in some of the nation's top schools like Harvard. In general, the movement believed more in spiritualism than organized religion, that the goal of humans was toward a spiritual state that literally transcended the physical and empirical world -- thus the path to enlightenment needed no intercession from organized religion or religious leaders, and was individually based on the human need for spiritual ascension (Gura, 2008).
Primary examples of this movement can be found in the 1836 Nature essay and subsequent 1837 speech to the Phi Beta Kappa Society by Ralph Waldo Emerson:
So shall we come to look at the world with new eyes. It shall answer the endless inquiry of the intellect, - What is truth? And of the affections -- What is good? By yielding itself passive to the educated Will… Build, therefore, your own world. As fast as you conform your life to the pure idea in your mind, that will unfold its great proportions. A correspondent revolution in things will attend the influx of the spirit (Emerson, 1837)
Spirituality becomes even more relevant for the later transcendentalists like Walt Whitman who, while using material from Christian sources, finds the concept of religion to be far more complex than the belief of one or two faiths even taken in congruence. Using Biblical allusions and innuendo, Whitman forms the very backbone and template of the idea of removing religion from spirituality, of individual communing with the process that is God, and of private and humanistic philosophical movement that will allow humans to reach their maximum spiritual potential. This is clear in his poem, Song of Myself:
1 - I celebrate myself, and sing myself,
And what I assume you shall assume,
For every atom belonging to me as good belongs to you.
I loafe and invite my soul,
I lean and loafe at my ease observing a spear of summer grass.
My tongue, every atom of my blood, form'd from this soil, this air,
Born here of parents born here from parents the same, and their parents the same,
I, now thirty-seven years old in perfect health begin,
Hoping to cease not till death.
Creeds and schools in abeyance,
Retiring back a while sufficed at what they are, but never forgotten,
I harbor for good or bad, I permit to speak at every hazard,
Nature without check with original energy
3 - Knowing the perfect fitness and equanimity of things, while they discuss I am silent, and go bathe and admire myself.
Welcome is every organ and attribute of me, and of any man hearty and clean,
Not an inch nor a particle of an inch is vile, and none shall be less familiar than the rest (Whitman).
Thus, the stage was set and the long lineage of religious change shown within the New World. The idea first of paganism, of polytheism and the worship of nature as the primary balance within the spiritual world; the use of one religion, Catholicism, to identify and justify the conquest of the new land; the rush to the new colonial world to establish a counter orthodoxy to Catholic European thought; the move towards a separation of church and state and a belief in humanism; finally to a movement that focused far more on spirituality and the path of the individual than staid and hierarchical concepts that resembles more the idea of the indigenous symbiosis of human and universe than any fundamental orthodoxy.