Many different factors contributed to the different types of freedoms enjoyed by specific colonies in British North America. The first was religious. Many of the colonies in the northern United States were founded by dissenters. Some, such as the Quakers, advocated religious freedom, but others, especially the Calvinists, tended to advocated limiting religious freedoms even more than they were restricted in England.
The plantation economy of the south made slavery profitable, something that was not the case in the northern cities that profited more from trade and manufacturing and had less agricultural economies.
Finally, many colonists were inspired by the ideals of the Enlightenment and saw those as a basis for founding a new sort of nation that was based on greater individual liberty and equality.