Do you feel that the prejudice suffered by the Catholics in Massachusetts contradict the ideals that founded the area?
There were some basic ideals of democracy involved in the founding of Massachusetts, although the Pilgrims were just trying to be practical more than to uphold some near and dear principles. As far as religion was concerned, they only practiced religious freedom for themselves, and openly persecuted those of even slightly varying faiths. Catholics had had a rough go of it in England, and in the New World as well, hence the founding of Maryland as a potential distant haven.
When you talk about the ideals on which the area was founded, I assume that you are talking about the Pilgrims' ideals since they were the ones who founded the Massachusetts Bay Colony. If so, I would argue that prejudice against Catholics did not contradict those ideals in any way. The Pilgrims did not come to Massachusetts for religious freedom. Instead, they came so that their religion could dominate all others. They did not want freedom of religion. Instead, they wanted the freedom to have their religion rule them.
The Pilgrims/Puritans were notoriously intolerant in religious terms. They ejected such people as Anne Hutchinson from their colony for holding incorrect beliefs. They even executed some Quakers for holding their beliefs. This shows quite clearly that they were not interested in modern ideas of freedom of religion. In fact, the word "Puritan" referred to their desire to "purify" their church of all Catholic influences.
So I do not think anti-Catholic prejudice contradicted the ideals on which Massachusetts was founded.