Also right now I have 10 external trade routes...still losing over 40 Gold per turn. That's with 12 cities and all of them have stock exchanges. I did not unlock Commerce though. I captured Big Ben from Theodora.
How anyone can manage a large empire and large military without having MASSIVE gold negatives is beyond me. I have units disband all the time from lack of money. I have to keep making more and pillaging/repairing every enemy tile I have a unit on in order to prevent it from happening. Liberty+Pyramids = 1 turn worker repair = totally super duper awesome
It could be because your capital and your cities are small in size. Most of your income doesn't come from trade routes or buildings or tile gold it is actually from city connections. (i.e. road or harbor connection to the capital).
The equation on this that determines your gold income is dependent on both the size of the capital and the city connected to the capital. Focusing growth is the best way to boost city connection gold.
Gold output = (City population * 1.1) + (Capital population * 0.15) - 1
For example, with a capital of 6 citizens,
a city with 4 citizens produces 4.3 gold per turn,
while a city with 5 citizens produces 5.4 gold per turn.
That is from the Civ Wiki. So it takes about 7 population in the capital to gain 1 gpt from connections.