And yet, from their own point of view, the position of the Puritan rulers was totally illogical.

While suffering from persecution in England, they had appealed to liberty of conscience; and when dominant in America the denouncers of persecution turned persecutors.
A spirit of resistance on the part of many was the natural consequence of a position so full of contradiction.

Instances of contumacy happened with such frequency and determination as should have given warning to those in control.

In November, 1631, Richard Brown, an elder in the Watertown church, was reported to hold that "the Romish church was a Christian church." Forthwith the court of assistants notified the Watertown congregation that such views could not be allowed, and Winthrop, who went in person with the deputy governor, Dudley, used such summary arguments that Richard Brown, though "a man of violent spirit," thought it prudent to hold his tongue thereafter.
In November, 1634, John Eliot, known afterwards so well for his noble work among the Indians, in a sermon censured the court for proceeding too arbitrarily towards the Pequots.

He, too, thought better of his words when a solemn embassy of ministers presented the matter in a more orthodox light.
In March, 1635, Captain Israel Stoughton, one of the deputies from Dorchester to the general court, incurred the resentment of the authorities.