The Pilgrims at Plymouth Bay Colony were Calvinists and Puritan Separatists, while the Puritans at Massachusetts Bay Colony were determined to reform the Anglican Church from within. While both were Protestants and Puritans, they had different goals and beliefs.
Most Puritans wanted to purify the practices of the Anglican church, preferring to reform it from within to remove all taints of Catholic worship. Many of these Puritans started the Massachusetts Bay Colony in order to build their City on a Hill, a church other Puritans might see as a model. However, the Pilgrims had determined in the late 16th century that the Anglican Church was beyond reform. Therefore, they had seceded entirely from the Church, many of them moving to Holland prior to emigrating to the American Colonies.
While these differences seem minor, it was easier for the Massachusetts Puritans to obtain funding and the approval and protection of the British throne than it was for the Pilgrims. In addition, the Massachusetts Puritans were overall a more educated and wealthier group than the Pilgrims, who were mostly artisans and farmers. This led, over time, to more prosperity and much faster growth for the Boston-Salem area. In 1691, the still-small Plymouth Colony merged with the Massachusetts Bay Colony to form the Province of Massachusetts Bay.