New Amsterdammers didn't always get along with each other, either. On December 27, 1657, residents of the town of Flushing, in what became Queens, formally challenged the fiat by New Amsterdam's director-general Peter Stuyvesant against practicing Quakers and his public torture of a convert to Quakerism. New Amsterdam had earned a reputation for tolerance toward ethnic, racial, and religious diversity, but there were limits. The settlers' response to Stuyvesant, an orthodox Calvinist, became known as the Flushing Remonstrance. It was vital antecedent of the provision in the Bill of Rights for freedom of religion, which would be forged in the following century in New York. Their petition is considered especially noteworthy for two reasons: It rebuffed, respectfully, a demonstrably intolerant public official who was not receptive to criticism of any sort; and unlike so many other divisions in New Amsterdam, it was not motivated by personal animus. It was, without equivocation, a matter of principle."If any of these said persons come in love unto us," the Flushing residents wrote, referring to the Quakers, "we cannot in conscience lay violent hands upon them, but give them free egress and regress unto our town." In other words, Quakers who came in peace would not be harmed. The gist of the remonstrance was straightforward; while Stuyvesant claimed that Quakers were spiritual seducers, New Amsterdammers were supposed to respect all the faithful:“We are bound by the law to do good unto all men, especially to those of the household of faith. . .. And though for the present we seem to be unsensible for the law and the Law giver, yet when death and the Law assault us, it we have our advocate to seek, who shall plead for us in this case of conscience betwixt God and our own souls; the powers of this world can neither attach us, neither excuse us, for if God justify who can condemn and if God condemn there is none can justify… The law of love, peace and liberty in the states extending to Jews, Turks and Egyptians, as they are considered sons of Adam, which is the glory of the outward state of Holland, so love, peace and liberty, extending to all in Christ lesus, condemns hatred, war and bondage.”The Flushing townsfolk made clear they were not being rebellious against New Netherland or the Dutch Retormed Church; just the opposite. They wrote that their position was "according to the patent and charter of our Towne, given unto us in the name of the States General, which we are not willing to infringe, and violate." That patent--issued in 1645, when most Flushing residents were English-granted them the right “to have and enjoy the liberty of conscience, according to the custom and the manner of Holland, without molestation or disturbance.”Governor Stuyvesant disagreed. He jailed the town clerk, then banished him from New Netherland. The town government was replaced with Stuyvesant's acolytes. Finally, after Stuyvesant was rebuked by the Dutch West India Company directors for mistreatment of Jews and just before he was dethroned by the British, they warned him to retrain from further religious persecution. Built in 1694 by John Bowne and other early Quakers, the Old Quaker Meeting House still stands in Flushing, a simple rectangular building framed by oak timbers and topped by a steep-hipped roof modeled on medieval Holland. It is said to be the oldest house of worship in New York.
The Charter of Freedoms & Exemptions stated that “no other Religion shall be publicly admitted in New Netherland except the Reformed, as it is at present preached and practiced in the United Netherlands”.
Stuyvesant wanted to preserve the true Dutch Reform Church in New Amsterdam as the only religion in the colony. As more people settled, this became quite difficult. He fended off the Lutherans when they requested a minister. In 1654 23 Jewish refugees arrived from Brazil. Three years later 12 Quakers from Yorkshire landed on Long Island and two women began preaching in New Amsterdam. Stuyvesant next tried confiscating vessels carrying Quakers to the colony, imposed a 50 pound fine on anyone shielding a Quaker in their house. His treatment of Quaker Robert Hodgson, preaching in Hempstead who refused to doff his hat in court was so barbaric that Stuyvesant's sister Anna Bayard intervened and saved Hodgson's life and thirty of his neighbors banded together to draft the Flushing Remonstrance. By 1663, the Dutch West India Company which sorely needed immigration, directed Stuyvesant to allow everyone to have his own belief.