Religious tolerance is a measure of how tolerant a country is of subjects of other religions. It is characterized by a set of sliders on the religion screen. A low tolerance of a religion is a source of revolt risk.
Setting Religious Tolerance
Religious tolerance is set on the religion screen for your country.
Depending on your state religion, and whether or not particular major religious events have happened, you'll get three or more religious tolerance sliders. Christian countries start with 3 sliders in 1419, but get more as Catholicism splinters. Most other countries get 4 sliders, some get 5, and pagan countries get 6.
For the most part, tolerance of a particular religion is set only by a slider of the same name. However, there are a few exceptions. Muslims and Orthodox countries eventually get a slider for "Protestant", but not "Reformed"; for them Reformed are tolerated as Protestant. For non-Muslim non-Christians, the slider for "Catholics" is actually tolerance of all Christians; similarly both Sunni and Shi'a Muslims are tolerated the same by non-Muslims.
Otherwise, if you don't have a slider for a religion, then you cannot control your tolerance of it, and automatically tolerate it at the middle level (+1 RR).
Religious tolerance in EU2 is zero-sum. If you tolerate one religion more, you must tolerate some other religion less. (And contrary to what one might think, you can be no more or no less tolerant regardless of the position of your innovativeness domestic policy.)
Effects of Religious Tolerance
The primary effect of religious tolerance is in raising or lowering revolt risk in all cities that a country controls. A high tolerance of a religion will lower the revolt risk. Here are the effects on revolt risk, according to the 11 slider positions:
Slider position [left . . . . (.) . . . . right] other religion RR: +11 +8 +6 +4 +2 +1 0 -1 -2 -3 -4 state religion RR: +22 +16 +12 +8 +4 +2 0 -1 -2 -3 -4
Religious tolerance also causes small monthly changes in your diplomatic relations with other countries. Relations increase only if both countries have their tolerance high for the other country's state religion. Other conditions must be satisfied for relations to increase over time, such as low badboy for the countries in question and no CB existing for either country against the other.