This has probably been discussed in another post, but I will chip in my own experiences.
Province loyalty depends on a few things such as:
1. Religion: the more people of the same religion as you, the more loyal the province. Use priests/alims to convert the population.
2. How long you've held the province. The longer the better.
3. Some provinces are a lot more rebellious than others. Livonia, Portugal, Scotland, Ireland, and to a certain extent Prussia and Lithuania are rebellions waiting to happen. E.g. in my last game as the Russians in high, expert, I had held Livonia for 50 years and it still rebelled with a 400-strong garrison, just because the governor got a -40% happiness vice. (It had BF but no church.)
A special case are provinces owned by the Papacy. If you bump off the Pope and hold his provinces, he will reappear in one or more of them no matter what you do.
4. As referred to above, the governor's vices and virtues, namely the ones that affect happiness. Also the governor's dread. Assign a 4+ dread governor and you will likely subdue any disloyalty in a province, provided it has a sufficient garrison. After conquering a province, I assign the general with the highest dread as governor, and only later swop him for a guy with high acumen.
5. Building a watch tower+border fort and a church in a province will increase loyalty significantly.
6. Your king's influence affects province loyalty as well. The more the better, obviously.
7. Contact with your king. If a province island has no line of ships connecting it to your other provinces, it will lose loyalty.
8. Enemy spies reduce your provinces' loyalty. Build border forts or post spies to counter them. You will most likely need at least a 2-star spy to catch enemy spies if a province has no border fort.
9. Tax rate. The higher the tax rate, the more discontent the population.
IMHO, the best way to keep a rebellious province in check is to place a spy of your own in there. Even a 1-star spy can work wonders.
I hope this helps.
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