The tolerance level is also very important if you want to convert a province to your state religion. Let’s say you play a Sunni Muslim country like The Ottoman Empire. Then you will probably have Sunni Muslim, Shiah Muslim and Orthodox provinces within your borders and if you start to expand into Europe you will get a few Catholic and Protestant provinces as well. This will cause a lot of rebellions, because you can never please all those different faiths with the “Zero-Sum” tolerance level, especially if your stability drops for some reason.
You will have to convert one of those faiths to “The True Faith”, and that is of course yours.
For example, let’s say that Transylvania is Protestant, and you want to convert them into a Sunni Muslim province (your state religion). Lower the tolerance level towards Protestant provinces to Zero. This will make them rebel. You will mercilessly fight down the rebellion and this will make the province’s population drop. Keep up with this “righteous” treatment of the people (it’s for their own good anyway

) until the province’s population drops just below 5000. Now send a colonist, or several, until the population reaches 5000 again. Voila, you have just turned Transylvania into a Sunni Muslim province!
Keep in mind though, that if you have several provinces that you have lowered your tolerance level towards they will also rebel, so be sure to have them surrounded by your holy crusaders!
The tolerance level towards different faiths also affects your diplomatic status. If you play a Muslim country, you will find that Christian countries will have a very low diplomatic score towards you.