After winning a province, the people are dissatisfied with the new owners, and you get high revolt risk. I think that the Unlawful Territory flag gives you additional revolt risk. If any group of rebels successfully takes your province, there will be a prolonged period of elevated revolt risk (nationalism, etc). High war exhaustion will increase revolt risk. If you collect War Taxes, that adds to War Exhaustion. Then, other nations can send spies to "Support Revolt" which will also raise your revolt risk if they succeed.
Some of these can be prevented. Until you complete your WC, there's going to be someone to send spies. If you let rebels take your province, that's your own fault. Waging war carefully can hold down your war exhaustion, because WE is higher if you lose battles than if you win. Revolt Risk will decline gradually over time by itself, but some of that is the War Exhaustion declining over time. As mentioned before, other ways to minimize revolt risk are increasing nation stability, building courthouses, and a local standing army. You can also hire a High Judge advisor to cause a certain drop in RR per advisor level. [High Judge does not make the RR go away, he just masks a few percentages of its effect!] It is difficult for a small nation to justify hiring High Judge when there are so many other things to do (Land Tech & Stability). RR directly reduces a province's income, so if a large nation has widespread RR, a High Judge can do wonders for your economy.
Furthermore, you do not *have* to collect War Taxes. I generally wage war without war taxes. When I go to war, tech research may get reduced or stopped when I go to war so that I do not run deficits. Yes, that gets me inflation through minting. I'm much more willing to struggle with inflation than I am to struggle with rebels.