Issos
Chieftain
Really, I have no intent on starting a flamewar, but it's quite obvious protestant countries enjoyed more religious freedom at the time, which reflected in an increased scientific progress.
Now, it's an interesting historical debate wether that was only for religious/cultural reasons or not, but the different progress in Europe between latin/mediterranean countries and northern ones is a fact.
After all, Galileo lived his last years as a prisoner, at the same time that Descartes lived freely in Holland and Sweden.
There are exceptions to this, such as Calvinist Switzerland (as I noted before).
And I think you're forgetting in RFCE no civ is forced to switch religions, they just have a different modifier (probability) for choosing when Printing Press is discovered.
1 - Nor do I but.. it's just not true. Try to be catholic in England during Cromwell revolution. I bet Your life would be way more painful, and most probably shorter, than one of protestant living in catholic Poland in the same period. Or even in France after stabilization of absolute monarchy. It's just a myth repeated all the time, that protestant were more tolerant for other religions/christians. Their organisation was weaker than roman catholic, but society pius enough doesn't need help of organisation to purge the heretics.
2 - There was such difference, connected with religion and culture, and many other factors. But i think it should be represented by each civ own bonuses and handicaps. Both protestant or catholic Spain should be more influenced (in bad way, but not only) by it's religion, otherwise Netherlands or France (there religious wars were rather casus belli to empower the king).