Alea-that brings us back to economics
Until larger nation states existed, those who would lead in Europe needed the religious power that the church conveyed. The new, large nation states of Europe were woven together by the richest, most powerful lords-growing rich from the reemergence of trade, and thus able to finance wars that lasted years. Once the larger nation states emerged, they could disregard edicts from Rome, and even leave the Catholic Church, as England did. So, from 1077, when Pope Gregory VII was able to force Henry IV of France to walk barefoot through the Alps to apologize for challenging the Popes investiture rights, to Pope Innocent III's reign when he placed all of England under Interdict, and made King John a vassal-things changed quickly such that by 1302, King Philip IV of France actually arrested Pope Boniface VIII. After that, when a lightning bolt did not strike Philip down, the mystique of church power was broken.
If Philip can arrest a Pope, certainly it was safer than had been thought to criticize the church. Those early criticisms helped foster the real world inquiry that gave birth to scientific thought.