Well, it certainly dident help that the merchant and professional classes took to Protestantism quite readily across much of Europe (hence it's political rise mainly in the Hansa, Neatherlands, and Scandinavian Baltic Sea trade zone). If the historical political clashes between the rising "commercial" forces with their newfound wealth and the entrenched land-rich but constantly indebted landed gentry still occur, than the later might not be so hard line on remaining Catholic as a sign of loyalty to the old regime and stiffen their alliance with the monasteries to protect land privileges and insure the continued dominance of in-castle retainers and monks over crafts as opposed to the better organized and efficient guilds/trades men's associations.
Still, it ended up as their lose when they started exiling the dissidents and creditor Protestants like they'd already done with the Jewish moneylenders/scholars before them. The massive brain drain and urban decay really dident do Catholic Europe any favors when it came to surpassing the feudal economy and ultimately proved a huge shot in the arm for the Dutch, Swedes, and Ottomans in starting up their colonial Empires and trade dominance in the Americas and Indian Ocean, creating the long-held distinction between the Papal "Land" and non-Papal sea Emperors.
Or, to quote Bayezid II "Those who piously say 'I am a most a Catholic Prince" are indeed fools; for they send willingly to me, his enemy, their national treasures. The physician, the tinkerer, the master of monies and craft: all are now his enemies' to command."