The Baroque artist from a Protestant country who famously did NOT produce work for the Catholic Church is
Rembrandt van Rijn.
While some Baroque artists from Protestant countries, like some Dutch painters, occasionally received commissions from Catholic patrons, Rembrandt's patronage came primarily from private individuals, civic organizations, and wealthy merchants within the Dutch Republic, which was predominantly Protestant. His subject matter was largely focused on portraits, landscapes, genre scenes, and depictions of biblical stories in a way that resonated with Protestant values.