You're confusing the French War of Religion in the 16th century with the genocide of Catholics by the French Revolutionaries in 1793.
By the 1790s the Vendée was heavily Catholic.
The Vandee is a complex situation involving several mass killings ~ even during the French Revolution. But peasants were, in general, neither nobles nor Protestants in that part of France.
As I recall Carrier was drowning peasants so they would no longer try to support local nobles.