There were many contributing factors leading to toleration of religion in Colonial America. One contributing factor was the over zealousness of the Puritans to create a City on the Hill in Colonial Massachusetts. The Puritans quest to create a perfect society based on Calvinist beliefs only created a society ripped apart by tension, anxiety and fear. A society destined to fail. The result of this rigid society was a quiet rebellion that spread among the second generation. 
Time Line Facts
The Mayflower had 102 passengers and 30 crew crew members. The ship was crowded. Conditions on the ship were terrible. There was no bathrooms. People were seasick. It took the Mayflower 9 1/2 weeks to cross the Atlantic to the New World. When they arrived in Provinceton Harbor, the pilgrims named the landing area Plymouth.
The Puritans who settled in Colonial Massachusetts were a dissenter group known as Separatists. This group of colonists left England fleeing religious persecution. Separatists believed that the Anglican Church or Church of England resembled the Roman Catholic Church too closely and was in dire need of reform. Puritans sought to purify the Anglican Church and to create a perfect society based on religious order. This society would be a community modeled on Biblical ideals with strict morals. They thought government should be a theocracy with laws based on Protestant teachings. The intentions of the Puritan colony was to build a city on the hill. This city on the hill would be a place of perfect holiness where everyone accepted the same church, the same morality, and the same God.  The Puritans believed as their oppressors did, that State sanctioned religion insured a bond between society and government maintaining order and stability. Allowing more than one religion would threaten the stability of society. Therefore, they did not grant religious liberty to anyone. This fact contributed to the growing movement towards religious toleration. It was noted in an article printed in 1776 in the Massachusetts Spy, quote It is the principle that every religion which is persecuted, becomes itself persecuting, for as soon as by some accidental turn it arises from persecution, it attacks the religion that persecuted it, not as a religion but as a tyranny. Compulsion, instead of making men religious, leads to hypocrisy. end of quote 
The Puritans were able to maintain the State Church because in Colonial Massachusetts communities and towns were close to one another.  This closeness ensured religious conformity. People kept close watch on their neighbors for sinful behavior. The result was widespread paranoia, tension and anxiety. Second generation Puritans grew up watching their parents live a miserable life seeped in suspicion. This indirectly worked at loosening the standards of the established Church in Colonial Massachusetts. When it was time for the second generation to join the Church, they refused. Membership in the Puritan Church involved going through conversion to become a saint. Conversion involved over a year of public humiliation.
Baptism was important to the Puritan faith because they believed it was necessary for salvation. The Puritan faith only allowed baptism of babies born of Saints. When the second generation began to have children, it upset the order of society. Since the second generation refused to suffer the ordeal of conversion, they not only condemned themselves to hell but also their children. The older generation could not have their grandchildren forego baptism therefore rules changed to accommodate the baptism prerequisites.  Gradually religion lost its grip on the population. Subsequent generations began to display signs of apathy towards religion. Samuel West who was a revered and highly influential clergyman from Dartmouth, Massachusetts in 1776 noted the change in attitude among the populace towards religion. quote Though I confess that the irreligion and profaneness which are so common among us gives something of a damp to my spirits, yet I cannot help hoping and ever believing that Providence has designed this continent for to be the asylum of liberty and true religion. end of quote 
Religious Persecution in the Colony
In the Massachusetts Bay colony, those caught practicing the Quaker faith were whipped, tarred and/or hanged.  William Rogers chastised the Puritan Colony for refusing to allow freedom of religion after they had experienced religious persecution when he wrote his book The Bloudy Tenant of Persecution for Cause of Conscience.  quote The blood of so many hundred thousand souls of Protestants and Papists, spilt in the wars of present and former ages, for their respective consciences, is not required nor accepted by Jesus Christ the Prince of Peace. end of quote  William Rogers founded Colonial Rhode Island on the principle of separation of Church and State guaranteeing religious freedom to all who settled there. It became a safe haven for persecuted Jews, Quakers and Presbyterians who had fled the Massachusetts Colony. 
The Role of Women in Puritan Society: Historical
Status, Marriage: Way of Life: Laws, Beliefs: Status, Evil, Sinners
Marriage: Family Life
Women were not scarce in Massachusetts. The Massachusetts Colony had immigrated into family units. there was a balance between the sexes. The Puritans believed in a covenant. The had a covenant with everything, God, wife, husband and so forth. Colonial women had to submit to their husbands. They were not aggressive or assertive. Women were suppose to be protected and they were. There were laws to protect women from spousal abuse. Although some laws were good springing from the idea of women being frail, other beliefs were life threatening.
Witchcraft: Feminine Soul: Satan: Superstitious Beliefs
The Puritans believed that the soul was feminine, weak and frail and susceptible to the devil. It was thought that women were susceptible to being witches. The devil attacked the soul through the body. A womens body was weak and frail. Together with a feminine weak soul, a woman was more apt to be a witch than a man. Colonial women who were assertive and aggressive were accused of witchcraft. Colonial women who had the outward appearance of masculinity were accused of being a witch. Being unfeminine was defined as having small breasts or childless. If a man possessed unusual strength, he was accused of witchcraft. Women accused of witchcraft underwent a physical exam by other women in the town or village. A mole, a wart or any form of a lesion found on the body of the accused witch was proof. These lesions were called witch's tits. It was thought that devils sucked at these tits.
If a woman did not conform or fit in with Puritan ideas of womanhood she was forced to recant. A woman who did not submit to her husband was subject to being called out a witch. If a woman admitted she was a witch to save her life, she admitted she was weak and frail susceptible to Satan. The admittance further demonstrated weakness because she proved she was too frail or weak to endure the trail and her execution. A no win situation. Often times, admitting witchcraft did not save their life, the judge who promise to spare the life of the accused would not be the judge residing the sentencing. Colonials believed that they were doing the witch a favor by burning her at the stake they were cleansing her soul.
Major Themes and Key Points: Chief Beliefs, Values, Customs
The soul is feminine
Soul was insatiable and consonant with the unappeasable nature of women
Satan Assaulted the body to conquer the soul
Devil could reach women's souls more easily
Weaker bodies compounded with the weakness of a feminine soul made it more likely that a woman would submit to Satan.
The vulnerable unsatisfied and yearning female soul was passively waiting for Christ but susceptible to Satan.
Woman frail submissive passive
Witches made an aggressive choice to conjoin with the devil thus aggressive and assertive women were pinpointed as witches.
The image of women as defined by Puritan values was evil and sin: Eve tempted Adam
Satan's powers corresponded to the Puritan earthly perception of women's bodies and souls.
gender nature of the social universe corresponded to supernatural behaviors and powers
The body was the most vulnerable part of one's total being, it was the body that succumbed to temptation and committed the sin so this was the battlefield between Satan and the Puritan.
Sinful temptations devised by Satan such as carnality, drunkenness and licentiousness provoked the body and threatened to lead it astray and let Satan take over.
Stronger body less likely to submit to devils temptations.
Body's lustful desires overwhelmed the will
The body as well as the soul had to suffer for sin.
As a consequence of Original sin and subsequent sin the body was punished by bad health.
A strong body could endure enormous suffering
Upon conversion the soul was protected by Christ.
Conversion was when the soul gave itself over to Christ.
Possession by Satan was enslavement
Either with Christ or with the Devil there was no in between
Satan designed his attacks according to his quarry
Weak body and vulnerable soul could also encourage ones faith in God.
Illness was only for the good of the soul
see Colonial Rhode Island for more information on the New England Colonies