catholicism and protestantism have a very interesting relationship and makes it very difficult to figure out - esp. in how to represent it in the game. firstly though, there was already schisms in christianity long before protestantism - with the orthodoxy and nestorians in the east. catholicism and protestantism, however, made large historical influences in the western world, including western europe and the americas, which i guess is where most of us r from, thus our slightly biased views on it.
either way, for the non-christian, it's easy to to see catholicism and protestantism under the same umbrella - i mean, they seem to share similiar histories, have the same God. it's only under a more westernized Christianized lens that u can see large diff. between the two among other seemingly "Christian" religions including mormonism, jehovah's witness, etc. in the americas (both us and north/south america) and europe since the 16th century, catholicism and protestantism had often been pitted against one another, whether it be through actual wars, politics, etc. so that, again, from a more western view, it's understandable to see why many wud see the two as two separate religions.
heh to be honest, i'd focus more on removing confucianism and replacing it with another religion (not only is confucianism not a religion but a philosophy, but it easily coexists with buddhism and daoism in asian countries - perhaps if we had animalism or some sort of native american, mesoamerican, or african religion represented instead)...