People who professed Christianity but disagreed with the Roman Catholic church (e.g. Protestants) would have been seen as worse rivals to the Roman Catholic regime than those who didn’t profess Christianity, such as Jews. Still, the latter didn’t dare oppose the Roman Catholic church or they, too, became fodder for the slaughter.
And this is one of the saddest chapters in Christendom. A congregation that was supposed to be exalting Christ ended up exalting mainly itself. It is so easy for a religious system to slide into such self adulation. Let us pray that evangelicals will resist such a siren song because the devil doesn’t discriminate, he tempts them in that manner too, resulting in a plethora of “Our Church Congregation Is The Only One Right With God.”
while other actions fit what you are saying, the spanish inquisition did not — it did execute 120 Protestants (too many), but the main target were conversos and moriscos, not Protestants