I am mainly interested in what modules you can make money from as they are
expensive. I just built a city and assumed that because they many modules
charge fees that the money goes to the owner. This has not been the case for
me. Is there any way to make money from shops, harbors etc? Or is it a question
of me needing to build a specific module to access the fees?

When you found a city you can start from the supposition that it will never
ever even go break even with the expenses (not to mention making profit).

For example, Orion is one of the cities that has made most income with 100M
which equals into 25% of its estimated total invested value in stock-listings
(yes yes I know not all these are from city founders but still). Orion has
been in game as long as I can remember and it made decade ago - with more
active players and more central location - 10-20x more monthly income than
cities earn today.

Answer to your question. Main income sources are shops, after that the set
fees from portal and bank. Rest you can pretty much ignore in that
perspective. For example harbors won't benefit city income.

Janitor of Macedonia,
Z
It just seemed like I wasn't getting charged for sabling my mount in my stable the day before. Now I am. No one has spent money at my city yet. So do you get charged for harbors and stables if you are the owner? Also what buildings do you need to keep protected from attack?