Old English þe (accusative and dative singular of þu "thou"), from Proto-Germanic *theke (source also of Old Frisian thi, Middle Dutch di, Old High German dih, German dich, Old Norse þik, Norwegian deg, Gothic þuk), from PIE *tege-, accusative of root *tu-, second person singular pronoun (see thou). The verb meaning "to use the pronoun 'thee' to someone" is recorded from 1662, in connection with the rise of Quakerism.
In Middle English, people began to use plural forms in all cases, at first as a sign of respect to superiors, then as a courtesy to equals. By the 1600s, the singular forms had come to represent familiarity and lack of status, and fell from use except in the case of a few dialects, notably in the north of England. People in Lancashire north of the Rossendale Forest and Yorkshire formerly were noted for use of the singular second person pronouns tha (nom.) and thee (acc.). For religious reasons (Christian equality of persons, but also justified as grammatically correct), the Quakers also retained the familiar forms.
Thou and Thee was a sore cut to proud flesh and them that sought self-honour, who, though they would say it to God and Christ, could not endure to have it said to themselves. So that we were often beaten and abused, and sometimes in danger of our lives, for using those words to some proud men, who would say, "What! you ill-bred clown, do you Thou me?" as though Christian breeding consisted in saying You to one; which is contrary to all their grammar and teaching books, by which they instructed their youth. [George Fox's journal, 1661]
While the Quakers originally adopted "thee" and "thou" on account of their grammatical correctness, they soon fell into the careless habit of using "thee," the objective, instead of "thou," the nominative. Common illustrations are: "How does thee do?" or "Will thee," etc. [George Fox Tucker, "A Quaker Home," Boston, 1891]
1510s, "permission granted by authority, licence," from French tolération (15c.), from Latin tolerationem (nominative toleratio) "a bearing, supporting, enduring," noun of action from past-participle stem of tolerare "to endure, sustain, support, suffer," literally "to bear" (from PIE *tele- "to bear, carry;" see extol).
Meaning "forbearance, sufferance" is from 1580s. The specific religious sense is from 1609; as in Act of Toleration (1689), statute granting freedom of religious worship (with conditions) to dissenting Protestants in England. In this it means "recognition of the right of private judgment in matters of faith and worship; liberty granted by the government to preach and worship as one pleases; equality under the law without regard to religion."
If any man err from the right way, it is his own misfortune, no injury to thee; nor therefore art thou to punish him in the things of this life because thou supposest he will be miserable in that which is to come. Nobody, therefore, in fine, neither single persons nor churches, nay, nor even commonwealths, have any just title to invade the civil rights and worldly goods of each other upon pretence of religion. [John Locke, "Letter Concerning Toleration," 1689]
Before any man can be considered as a member of Civil Society, he must be considered as a subject of the Governour of the Universe: And if a member of Civil Society, do it with a saving of his allegiance to the Universal Sovereign. We maintain therefore that in matters of Religion, no man's right is abridged by the institution of Civil Society and that Religion is wholly exempt from its cognizance. [James Madison, "Memorial and Remonstrance Against Religious Assessments," 1785]
Unlimited tolerance must lead to the disappearance of tolerance. If we extend unlimited tolerance even to those who are intolerant, if we are not prepared to defend a tolerant society against the onslaught of the intolerant, then the tolerant will be destroyed, and tolerance with them. [Karl Popper, "The Open Society and Its Enemies," 1962]