Civ IV is FAR FAR different from previous civs because of this very issue. In older versions, and AC especially, it was better to have 10 cities of 1 pop than 1 city of 10, simply because 10 cities of 1 works 20 tiles. In Civ IV, that "loophole" has not only been closed, its become a MAJOR factor in the strategy of the game.
The best rule of thumb I have seen is the "60%" rule. If you never touch the Science slider, it will drop gradually as you put up cities, and keep you as close to "even" as possible. Using the 60% rule, you STOP expanding when your slider goes to 60, and let your cottages and infrastructure build up some, maybe get some financial techs like Currency and Banking, and once you're showing a decent profit at 60%, you can begin expanding again, either by Settlers or by force.
Also, since it bears re-mentioning, check your cities to see which tiles they are working. Sure, that 5H copper mine is great for fasting buildings, and that 5F pig tile is awesome for growth, but you may need to switch to tiles that have some commerce so you can stay in the black. Coastal tiles, riverside tiles, etc, are critical to keeping your economy afloat. SPeaking for myself, Lighthouses and Riverside grassland Cottages are among my first targets in new cities, so I can get some commerce without starving when I need it. My current game is a perfect example. I over-conquered a neighbor after running my own "blocker" cities too far from home, and now I am paying the price for not razing a couple conquered and over-extending my block. Sure, once I get past it, the filler cities will make my empire goddly, but its a real challenge to overcome. And I am only playing Monarch. Gets harder to manage these things at the higher difficulties.