In chapter 3, Hofstadter dives into the meat of his thesis, the historical evidence for anti-intellectualism in America, beginning with religion. He reaches his key point 2/3rds of the way through the chapter, with this:
And here we have the nub of the difference between the awakeners and the spokesmen of establishments: whether it was more important to get a historically correct and rational understanding of the Book—and hence of the word of God—or to work up a proper emotion, a proper sense of inner conviction and of relation to God.
To recap: Somewhere slightly more recent than the dawn of time, there was the Church. There was only one Church, and it reached and controlled most of Europe. The upper class, healthy, and wealthy were chosen by God for their status; the lower selected - or doomed - to labor. And then, the climate shifted, cooling the land and producing fewer crops. Ships carrying infected fleas from China reached Europe, and the resulting plague killed off over a third of Europe's already hungry population - many of whom, it must be said, were not especial sinners and did not deserve God's punishment. Shortly thereafter, in an unrelated incident, politics within the Church split into two divisions, each supporting a different claimant for the papal seat.
Up until these phenomena, the average person fell in one of two camps: if a peasant, he or she probably worked all week planting, harvesting, tending livestock, tending children, and generally seeing to their household; if noble, he or she lived in a slightly larger wooden house, and personally saw to the household or oversaw the farming - certainly a better quality of living than actually doing the work, but not too far off the ground from it, either. Both classes tithed when necessary, attended church for their souls - and probably didn't give much thought or question to the teaching thereof. Children of the nobles sometimes went into the Church, sometimes as a matter of disposal, other times as a matter of actual faith.
The climate cooling and the plague epidemics, however, created questions of faith. Educated people, at least, began thinking more of the here-and-now than of the distant and far off after life. People in Southern Europe, with access to Muslim scholarship from northern Africa, re-printed and distributed math and scientific works, and this in turn spawned a trend in original in landowners outside of the Church - what we call the Renaissance.
And this, in turn, led to the Reformation, which would not have happened without the spread of scholarship, in particular, Humanist scholarship, and the discontent with the Catholic Church caused by Renaissance scholars questioning faith and the Church's practices. In particular, since the gap between the haves and have-nots for the first time in history was growing - there had always been a gap, even a great one, but for most of history, the nobles closest to the peasants lived almost as roughly as the peasants themselves did, tied to the agricultural cycle - it was becoming painfully obvious that the Church had two rules - one for the average person, who was expected to live as free of sin as possible and to atone for what sins they could not avoid; another for those rich enough to pay for indulgences, or forgiveness for their sins. And yet, the people of Europe were locked in, because the Church taught that the average person needs an intercessor, someone to plead their case with God, to teach them what He has said, and to fulfill the necessary rites and obligations for their life.
There can be little doubt that the conventional judgment is right: by achieving a religious style congenial to the common man and giving him an alternative to the establishments run by and largely for the comfortable classes, the Awakening quickened the democratic spirit in America; by telling the people that they had a right to hear the kind of preachers they liked and understood, even under some circumstances a right to preach themselves, the revivalists broke the hold of the establishments and heightened that assertiveness and self-sufficiency which visitor after visitor from abroad was later to find characteristic of the American people.
The Reformers dealt with the question of purchasing indulgences - forgivenesses - for their sins from the Church simply and efficiently: they made it part of their dogma that no earthly means of redemption is possible, only the grace of God can redeem. Although a scholarly contingent of Lutherans sprung up to counter the Jesuits, who had formed to fight the Reformation on a scholarly angle, the Bible was held to be the only divinely inspired book, and in fact, the only book necessary to read to understand the Word. It seems important to note that the Reformation was not an anti-intellectual movement; if anything, it was an anti-corruption movement and targeted the privileged instead of the educated. Their methods, however, had anti-intellectual results - specifying that the Bible is the only Word of God necessary in order to eliminate the human error inherent in electing a Pope as the human voice of God; preaching that God's grace is the route to salvation eliminated the notion of scholarship as a way to heaven just as effectively as it eliminated the idea of salvation as a product sold by the Church.
All of this religious reforming took place in the same centuries as the early colonization of the New World, and the immigrants who crossed the ocean and settled in North America were of a variety of faiths: Lutheran, Calvinist, Anglican, and yes, Catholic - and denominations and movements which grew out of them. The Puritans who settled New England grew out of the Church of England, which was itself a Reformation of the Catholic Church based on the infallibility of the Pope (and Henry VIII's desire for a male heir.) The Puritans believed, as did the Lutherans, in the individual's personal relationship with God and the lack of a need for professional clergy, but this did not prevent them from respecting scholarship and comparative philosophy. Harvard was founded by the Puritans in the Massachusetts Bay colony, and most colonies had passed a law mandating the hiring of schoolteachers.
Puritanism, as a religion of the Book, placed a strong emphasis upon interpretation and rational discourse and eschewed ranting emotionalism. Puritan sermons combined philosophy, piety, and scholarship; and it was one of the aims of Puritan popular education to train a laity capable of understanding such discourses.