I have a question of my own:
I know that wrong religion provinces (My state religion is reformed and a provinces religion is catholic) take penalties, right??
My question is: Do I have to convert them to the true faith so that they don't recieve penalties, or will the penalty go away if I'm, tolerant enough towards them?
Yes the negative (and positive) effects are tied to tolerance [see religion tab]. Tolerance affect tax revenue, revolt risk, stability cost and population growth. If 'true faith' and 'heretics' are equally tolerated, the comparative penalties go away. Still, this is hard/impossible to achieve, especially without reducing the tolerance of your 'true faith,' which may not be preferable.
In the case of the direct penalty to tax revenue, increasing tolerance of heretics/heatherns to 0 removes the negative effects. In this context they go away. Still, the
high tolerance to 'true faith' if you have avoided decisions lowering it in order to raise tolerance of heritics and so forth, will provide nice comparative bonuses to pop growth, stab cost, and revolt risk (which in turn affects tax revenue negatively if above 0 RR). Essentially, a very intolerant society favouring it's majority population will result in a more productive society -- in the provinces adhering to the true faith.
What I'm saying is: Yes, if you are tolerant enough, all negative penalties will go away, but if you compromise your 'true faith' in the process, which is what many decisions require, so will all the positive effects.
Depending on how varied your nation's religious landscape is, one is better than the other, but converting provinces is almost always good, even if you are very tolerant towards heretics. Often, the problem is the number of missionaries in my opinion.
