I believe that there was some Religious toleration in Colonial Massachusetts. Firstly, one must engage in the definition of tolerance and toleration.
Tolerance and toleration is often misunderstood between liberal legacy and impeded efforts to improve upon it. This term, "toleration", is really a set of social or political practices while "toleration" is a set of attitudes.
Works such as John Winthrop's City Upon a Hill, 1630 states that the society should "...walk humbly with our God, for this end we must be knit together in this work as one man…so shall we keep the unity of the spirit in the bond of peace, the Lord will be our God and delight to dwell among us…". This basically means that he wanted the Massachusetts Bay Colony to seek for a model religious and civil society based on a contract with God and one another.
On the other hand, the Massachusetts Puritans exhibited intolerant anti-toleration. This, targeted the non believers as well as ones who did not follow the specific theocracy exhibited.
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No. To be able to vote a man had to belong to the church and own land. One reason Rhode Island was settled is that people left, or were expelled, from Massachusetts and other New England colonies because they didn't follow the rules of the church and there they could. Ann Hutchenson is a perfect example of this thinking.
They moved from England because of their argument with England's rules of belief.