Catholics suffered discrimination in the colonies just as they do now worldwide.
Catholics made Christians suffer much worse under their "discrimination," like as Islam does now.
Canons of the Ecumenical Fourth Lateran Council (canon 3), 1215:
Secular authorities, whatever office they may hold, shall be admonished and induced and if necessary compelled by ecclesiastical censure, that as they wish to be esteemed and numbered among the faithful, so for the defense of the faith they ought publicly to take an oath that they will strive in good faith and to the best of their ability to exterminate in the territories subject to their jurisdiction all heretics pointed out by the Church; so that whenever anyone shall have assumed authority, whether spiritual or temporal, let him be bound to confirm this decree by oath.
But if a temporal ruler, after having been requested and admonished by the Church, should neglect to cleanse his territory of this heretical foulness, let him be excommunicated by the metropolitan and the other bishops of the province. If he refuses to make satisfaction within a year, let the matter be made known to the supreme pontiff, that he may declare the ruler’s vassals absolved from their allegiance and may offer the territory to be ruled lay Catholics, who on the extermination of the heretics may possess it without hindrance and preserve it in the purity of faith; the right, however, of the chief ruler is to be respected as long as he offers no obstacle in this matter and permits freedom of action.
The same law is to be observed in regard to those who have no chief rulers (that is, are independent). Catholics who have girded themselves with the cross for the extermination of the heretics, shall enjoy the indulgences and privileges granted to those who go in defense of the Holy Land. (http://www.fordham.edu/halsall/basis/lateran4.asp)