If -as a european faction- you conquer a city in the holy lands, it's better to always exterminate the people there, to keep them quiet long enough for you to build up churches and pump out priests who convert the holy lands to catholicism. When the religious unrest is gone you should be able to hold that city with an average garrison without haveing to worry about revolts. Sure, there's the distance to capitel thing too, but in my experience it's mostly the religion that causes trouble.