Well, assuming you don't have ports currently blockaded, start with the finances screen. Look at income and expenses breakdown, and see what's costing you a lot. Garrison units cost money, aside from up to 6 militia units in cities. That will eat up a lot. If your expenses don't seem unreasonably high, then I'd have to guess the problem is trade rights. Trade routes make more money trading with close neighbors than they do with far away factions, so if you're at war with your neighbors, you're losing out on money. You don't make as much money trading with your own cities as you do trading with foreigners. You're at war with Venice, so that's one of your trade partners. What about Milan, the Papal States, France and the Moors? Do you have trade rights with them? Have you taken Cagliari and Ajaccio yet? Rhodes? Capture them if you haven't, turn them into cities, and build ports as soon as you can.

Eventually the size of your empire reaches a certain "critical mass", beyond which point you do ok economically by trading with yourself. Up until that point, it can be very difficult being at war with your neighbors. You need to have one or two close neighbors where you have trade rights.