Why because Richelieu waged war on and defeated the Huguenots?
No, because Richelieu, Mazarin and Louis XIV's main objective was to shoot down the very catholic house of Austria (Spain), and they did so by helping the protestants in the Netherlands and Germany. They were men of the catholic church, but they allied with heretics (outside of France) to beat the dominant power of the same religion. The reason they waged war to the French hugenots was because these contested their authority, not because of their religion (the princes of the Fronde were catholic as well, and they did ally locally with hugenots to try to get power).
In a way, at the time, most of Europe was playing like the AI in Civ IV, and France was the human player who was using the AI routines to his advantage.
Anyhow... I don't like how religion plays out in CiV, but it's still a huge improvement over the system of Civ IV. It used to be the dominant diplomacy tool, now it's negligible in term of diplomacy (the choice between order/autocracy/freedom replaced it at the diplomatic level, which I still don't really like either). Now it became an extra social policy kind of system.
If only the AI could stop sending their annoying missionaries and prophets...
The most fun I had with religion was in a game where most of my opponents were very religion-biased (Celts, Byzantium...) so I didn't bother to build a single shrine and developed my empire without religion. At some point, my territory was covered with missionaries from 3 different civilizations, fighting to convert my cities, going back because a rival missionary had undone what they just did, and finally dying of attrition, while I was researching Flight... That was an amusing show.