That's not necessarily a problem, btw. Losing a lot of money and going into a hole is, but I often run for large parts of the game at a deficit, particularly on higher levels when I can trade for cash with the AI.
The question is: what do you want to do with your money? Are you trying to research fast? Are you trying to build up a large surplus to cash rush buildings or do a mass upgrade to swords/knights/cavalry/something so you can take over the world? Or do you just want to have as much money as is possible?
Aabraxan covered the specifics very well (as he always does
Understanding what your goals are is important - if you want to take over the world militarily, you may want a lot of barracks and not need so many libraries or temples. While have a granary in every city is nice, it's not even close to being necessary - 2 or 3 is usually quite sufficient. Building most cities on freshwater helps a lot, because you don't have to build aqueducts. Not building core cities in marginal territory is a good thing to do, because they can't get very big.
Luxuries are your friend, especially as you get to higher levels.
Temples/cathedrals/colloseums are not well designed by firaxis, in my opinion - they don't really help that much unless you have 0 luxuries and cannot trade for them.
Trade a lot with the AI - trade techs for gold and gpt and other techs and luxuries.
If you do build things like harbors (I suggest you do), make sure you make use of them!! There is very little use in building a harbor in a city that has no citizens working the coastal tiles. There is nearly no reason to build a library if you are going to run 0% science and almost no reason to build a bank if you are going to run at 0% tax. If the city won't produce units, don't bother with a barracks. If the city is in the inner core or is very, very corrupt, don't bother with courthouses. If the city is in the 2nd or 3rd ring, though, a courthouse can be the best thing to build!
Very few cities need airports - they are very expensive.
try to get your cities as large as you can without putting them into civil disorder. Don't let very corrupt cities going into disorder drive you to raise the lux tax. I rarely have the lux slider up beyond 20%, except very early in 20K games or if I have a fundamentally important wonder to build.
Expand - build at least 1 settler factory. Make sure you expand AT LEAST until you get to the "build the forbidden palace" message - try to get at least double the number of cities you had when you get that message.
Build the forbidden palace. This can have a large long term effect on the health of your civ.
Build fewer defensive units. In epic games, the human player can often do very well playing a crust defense - putting most units in border cities. 3 spears in your capitol is usually just a drain on the economy.