Always build more workers!  Wait, wrong game. 
 
How many cities do you have, what's your goal?  I find the best way to go about doing things is figure out the resources around each city and focus the city.  Don't just try to do everything at each city, but prioritize.  If you are going for a cultural victory, keep it small, no more than 3-4 cities, not counting puppet states.  
 
For example, designate a city that's your science-focused city.  Whenever you get a chance to build a national wonder that gives like +50% to science, build it there. 
Have another city designated just to pull in gold, set up a fair bit of trading posts around the area and get upgrades like markets or banks.   
 
Don't just build everything, figure out what you want the role of each city to be, and focus towards that.  You can favour some trading posts some more too, I find the computer is excessive about wanting to put down farms, I never need nearly as many as it wants to setup.   
 
Also, you may want to consider Commerce or Order social policies, which help with money/large empires respectively.  If you can lower your maintenance costs, it'll help a lot.

I'm not entirely sure, but I think workers (and other units) have up-keeps as well.  Try deleting a few, that may help.  Also, setting a city or two to turn production into gold after you research the currency tech might help.

Here's what I do: Don't build every building in every city. This seriously hurts economy. Just build what you really need in a specific city and keep your happiness around 20-30 (makes a buffer so you could invade one or two enemy cities while keeping building upkeeps low, since those buildings are quite expensive en masse) and expand on that area as needed. 
 
Traderoutes and that similar land improvement which name fails me also helps a lot. Oh, and I believe roads drains money too so build those sparingly (I could be wrong about this part, haven't occurred to me to actually check this).

" I'm about 500 turns into my game and my economy is in the dumps.  Every turn is a struggle to keep from going negative.  I think my problem is that i made pretty much all buildings(except for military buildings) in all my cities and the upkeep is killing me.  ...  I've built all the finacial structures up through stock market in all of my cities, i've been building cultural buildings because that should increase my borders which would open up more resources to me, i've got a bunch of workers improving the land, i'm not sure exactly what im doing wrong..."

Don't have a fiat currency. Back all money with gold and silver. Maintain a large manufacturing sector and don't export your jobs overseas. Make sure imports maintain balance with exports, unless deficits can be balanced in other ways. Don't tax your people too highly, taxes are first and foremost a burden. Keep a relatively open economy, let trade be fair and free from intervention. Don't manipulate the markets for narrow interests. Budget deficits must only be short term at absolute worst, and must be paid off within a few years of expenditure. Stimulate the flow and creation of ideas, so goods can be created.  Never let narrow agendas dominate the economy. Never become a war economy unless you're threatened with genuine invasion/obliteration, and even then the economy must be weaned off war funding once the threat ceases.
 
Oh, pardon me you were talking about Civ V....

Don't put your workers on auto. Seriously, they made my economy to minus 3 per turn because they made roads everywhere. I dont know if it's a bug or not, but i can recommend you to not do it.

...just like SC2, build more workers and place them in places that'll score you more gold.

Don't workers have upkeep? So then you'd have to figure out how many is enough.

" Don't have a fiat currency. Back all money with gold and silver. Maintain a large manufacturing sector and don't export your jobs overseas. Make sure imports maintain balance with exports, unless deficits can be balanced in other ways. Don't tax your people too highly, taxes are first and foremost a burden. Keep a relatively open economy, let trade be fair and free from intervention. Don't manipulate the markets for narrow interests. Budget deficits must only be short term at absolute worst, and must be paid off within a few years of expenditure. Stimulate the flow and creation of ideas, so goods can be created.  Never let narrow agendas dominate the economy. Never become a war economy unless you're threatened with genuine invasion/obliteration, and even then the economy must be weaned off war funding once the threat ceases. Oh, pardon me you were talking about Civ V.... "

Lol
Well, I always wondered why the computer would be able to have such a weak economy.

Building maintenance could never reach so high, the most expensive thing can always be the army.
I guess I can only share my strategy, against computer, it does never fails:

Your meta is reaching overpoped cities in a special 'combo' placement, such as having a industrious city with a couple of special resources that provides gold nearby. (i.e.: having a wonder that provides +5 gold in a coostal city with wales or pearls with boats + market + bank + stock exchange + East India company)
Focus on food, some social policies and some wonders, the more population you have in 1 city, the more gold you will get from them;
Don't place cities too near each other, if one city is able to get all the luxurious resources from an area, there is no need to make another one in the same region. No luxury resource = no city.
Latter in the game, if you have enough population in one city with the land properly improved, you will be able to use specialists that will improve your economy further. And latter on you will be able to get social policies from Liberty branch, such as lowering the food cost of specialist, further speeding your city grown and pop cap, and making room for more specialists to come in.

The first building I do is always the monument, and the first policy is the tradition tab. This is very important, otherwise getting social policies would be very slow for your early game and you would be like 30 or more turns behind in that way.

An interesting strategy is to play the game with only 1 city, make it overpopulated, focus wonder building and get the full tradition policy. The population + the policy gold bonus should be enough for you to be able to stand a entire army with a single city, while having it fully built.
Another strategy is to focus the piety policy branch and focusing early game in building up your religion with faith bonuses. Once you have the whole branch, each sacred site you have will give you plenty of gold and culture for any future policies you want to get too. Getting the Economy policy branch can also be helpfull principally if you have many gold specialists that to boost the number of great merchants, but the economy branch is very situational (like the landsneck policy that is good only if you are at war at the right era, or the wagons that is good only if you don't have access to sea from your main trade cities, or the road cost diminished that is good only if you have a great number of roads).

There are many ways to sustain a good economy, and very few ways to lose gold that much; actually to make someone lose that much gold would require certain military strategy.
The real challenge is actually to be a magician of the gold, to be able to fully build an entire city in 1 turn making it reach 10 pop in less then 20 turns. Be able to bribe every single nation of the game to get the votes you would like to see in the congress, save all your currencies and efforts without having any army and buying one when you need, making it pop in front of the enemies eyes out of nowhere while they slowly march towards your "defenseless easy" cities.

If you are having trouble with gold, you are probably not planning properly the place of your cities before building them.
Having a great number of cities can be economically bad actually, it is actually much more military and cientifically purposed. Still it is an interesting way to spend your money once you have an income, indeed, if that is your focus.

Production in Civ V is actually a boon when dealing with money because it can be converted directly into gold production. However your city population level is also a major factor in how efficient your land use and building use is. Without the pops your buildings could be unused or the land that generates resources could be sitting fallow. In a lot of cases it's important to focus growth first in cities to generate pops for use of building to their potential and improve output. This also helps generate more science since population is related to science production.

Trade routes are also important to plan. Longer routes and certain building types can vastly increase the power of trade units (ports and caravanserai). Shipping routes are also far stronger than land routes so you should be working towards having as many long distance sea routes as possible and have a trade port upgrade as well. Doing this should make it possible to maintain every building in your empire with 1 garrisoned unit in every external city and a small skirmish force even at Prince difficulty (upkeep costs go up as difficulty goes up).