That used to happen to me all the time. Here's what worked for me:
Be disciplined in your building. Even if you start with the money-making buildings, it's easy to lose track later on as you chase the big military structures. It's more fun, frankly, to build baron's stables all over the place than fairgrounds, but not as efficient.
I find I do OK as long as I specialize (one top-level artillery producer, one cavalry, one spies/assassins, one infantry, one missile troops, one religious center), then maximize money in the rest.
You need fairgrounds/ports/paved roads/markets in as many places as you can get them; you don't need an armourer except in your infantry and cavalry producing settlements.
The one exception is that I find cannon so useful that I tend to build a lot of basic gunpowder structures.
And I build at least two specialist finance cities: Merchants docks, great markets, anything that boosts trade, and the bigger the better, and create all my merchants in them to get a merchants' guild ASAP. One can also double as your primary dockyard, as there's a lot of overlap between ports and money.