A CA developer came by and mentioned causes of unrest, I think it was posted shortly after the game came out.

What your most likely reason is economic failure of the city, and even if it shows a positive # for income it still may be a failure.

Some of the reasons for bad econmics is farmland. Another is poor trade income.

Some cities are prone to it do to poor farmland and noone to trade with, no matter what you do. Also corruption can ruin a cities economic power.

Some cities are prone to it forever like Nepte and Palma. Nepte is hurt from multiple factors. Only 2 cities to trade with and with a small population merchants do'nt trade much with them, bundle this in with their poor farmlands and then the reduced income from corruption due too your not likely to even have a capital that's even close to them. Now Palma can be improved, unlike Rhodes who probbly have a bout 20 cities to potentially trade with Palma has a limited selection. Now I have never had a game last long enough to get Palma to get 3 trade fleets, but when you do it may kill the unrest as they have become economically stronger.

Now With Parthia never been near them before but because they are stuck on the edge of the map they get that special building of caravans I believe. Now at the edge of the map reduces trade partners but I'm guessing those caravans compensate for that.

Also if you move your capital to the edge of the empire you will notice an increase in unrest in the outer cities along with higher corruption.

Hope that helps