I think my experience with rebellions is linked to the self-changing tax rates, even in cities with governors (I don't auto manage those). If I move several units of troops out of a city, very frequently the tax rate will jump from normal or low to high, which almost instantly causes the little "happiness face" to turn blue or red and the populace starts tying nooses and eyeing the lampposts.
I'm still having a hell of a lot of fun (even with checking a lot of tax rates). I'm trying to conform my own strat with the senate's suggestions; so far so good (but I'm still only in 235 B.C.)