Collier20, he's trying to run a specialist economy, so cottages aren't the solution.
Well, except around the capital. You do need a source of income, so generally, in a SE, you cottage the capital, which is usually in a good location for that, and then you benefit from Bureaucracy's commerce boost.
Even so, cottaging the capital will probably not provide you with enough gold to stay solvent as your empire grows. My understanding of the SE is that you will need to almost constantly be at war. Pillaging and capturing cities, as well as tribute, will provide the other sources of gold for your economy. You should be out-teching your rivals, as well as out-producing them, so having enough advanced units to support war should not be a problem.
In addition, as you capture cities, you may consider cottaging another prime location for more income. A good example would be if you capture a rival capital which is also a holy city.
As Cam_H mentioned, markets can be useful if you want to run merchant specialists--though you could just switch to caste system and run as many of them as you want without that building. In fact, with your cities producing so little commerce, banks, markets, and grocers will be of limited utility--though you'll need enough banks (8, IIRC) to build Wall Street later on.
JackOfClubs has begun a good
beginner's guide to the SE in the Strategy Articles sub-forum--check it out!
