I can see why the American colonists were upset by the British going easier on the French 'Canadiens' than on them, but at least some of this is just plain bigotry. It's kind of ironic that many Protestants were concerned about freedom of religion when they themselves wouldn't provide it to Catholics.
More than a century later, these same religious conflicts erupted in post-Confederation Canada, when Orange Order Protestants wanted to forcibly assimilate Irish and Francophone Catholics. Apparently, their idea of 'freedom' consisted of everyone being free to follow the religion (Protestantism) and speak the language (English) that the Protestants wanted.