Winthrop and his deputy governor, Thomas Dudley, decided that the area around Boston Bay would be the best place to situate a large settlement, and before August was over the new arrivals had moved to Charles Towne, where Endecott had planted a small settlement the year before. That's where the first American meeting of the governor and general court took place, under a tree, on August 23. (If any picture was ever painted of this event, it apparently failed to make it onto the Internet.)
The meeting was attended by Winthrop, Dudley, and seven assistants. That body passed a law decreeing that the assistants alone would thenceforth elect both governor and deputy governor, and always from among their own number. This law clearly violated the charter, which granted every freeman a vote on who got to be governor, deputy governor, or for that matter assistant, and said that all freemen could be candidates for any of these positions.
Governor Winthrop hoped that the new colony would become as pure an expression of Puritan ideals as was possible on earth, and he was inclined to see an excess of democracy as an obstacle to achieving this end. He was ready to set about turning the ideal into a reality—the next business of the meeting was to provide for the building of houses “with convenient speede, att the publique charge” for two ministers. Clergymen might not be allowed to govern Massachusetts Bay, but their influence was always large, and their presence was necessary—it's impossible to imagine the Puritan “Bible commonwealth” functioning without them.
Not everyone was pleased by the religious restriction—the king and his government were outraged, of course, when they heard about it, but a good many devout Puritans in the colony also had reservations. Not everybody wanted to testify publicly to what might today be called a “born again” experience. Nothing of that kind was required by the charter, which Winthrop kept from public view as long as he could. Eventually, however, he had to yield to popular pressure and let it be read.
To those who objected to the unchartered religious requirement, however, he argued that—given the steady inflow of immigrants and the continuing expansion of settled areas—it would be impossible to conduct the colony’s governmental business in general meetings of all freemen. A governing body limited to church members would put all decisions in the hands of solid citizens who were good, orthodox Puritans. Massachusetts Bay might not be a theocracy, but under Winthrop’s system it would be a religious oligarchy. This satisfied most people.
One change that history textbooks don’t always mention took place as soon as the colony was established in the New World: although they continued to describe themselves as Puritans, the settlers of Massachusetts Bay became, by historical standards, not Puritans but Separatists. On this side of the Atlantic, they were in no position to exercise further influence on the Church of England, which they wouldn’t even allow to set foot in the colony, and there’s no evidence that the Puritan settlers kept to their original plan of purifying it. The church they founded in Massachusetts Bay was, like that of the Pilgrims in Plymouth, congregational rather than episcopal in organization, and in later decades that was the name used by the church established in both colonies: the Congregational Church. (It’s said that Thomas Dudley, who died in 1652, was the first to apply this term to the church, though he may have meant it as a description rather than a name.)