Well, trade makes tons of money. Good port cities are nice to have. I usually get communal farming, and that tends to pay for the garrisons in cities.

Territory is another one, the more terrirtories you have, the more profits you will make. I have noticed money being more tight in M2TW too. My solution has been to seek the large enemy cities, and then to sack them. In Egypts area, if I am a catholic faction, I use my ex-crusader armies to run around sacking cities and forget about holding them until they are at least 50% catholic.