Without more information about what you're doing, it's hard to tell how much of this you already know, so forgive me if I state the obvious. Funxus makes some important points about the importance of trade arrows within your cities, and how the city improvements (markets, etc) and terrain improvements (roads) can impact them. The way to avoid cash - and other - problems is to manage your trade well.
Representative governments (republic, democracy) produce significantly more trade than earlier governments, but you must also spend luxuries to manage your happiness so there is a tradeoff here, but in the long run it's usually worth it. Democracy eliminates the nasty corruption that eats away at your trade in republic, so it is much nicer.
Another thing to look at is delivery of trade goods caravans and freights. Delivering these to cities will give you a cash and science bonus upon delivery (more if the city demands that item), but it also sets up a trade route which can add even more arrows to each city, thus allowing the city to make more cash on an ongoing basis. This is the key to happy, growing cities.
Go read around the forums and especially look at the threads about trade, republic and democracy. Some of them are fairly detailed and in depth so you probably won't immediately grasp everything they talk about (I am still learning from many of them), but just try to get a general understanding of how to get trade working in your favor. When you start to understand these techniques you'll probably wonder how you ever had a cash-flow problem!