I actually feel bad for you.

Here you really try to learn and wreck your brain trying to understand what's going on it this game. I realize how weird these issues must seem to you, so I sympathize. Because all you wanna do is to master this great game.
The fundamental problem here seems to be that the developers of the game have chosen to make things so confusing. (I recall your earlier calls for help...) Its not that these things are complicated, really, but the way they are implemented can indeed be very confusing...
You really need to take a breather and look at this issue with some perspective. So the game has something called a Gold special resource, it also has Gold as currency, and there's this game concept called Commerce (which looks like gold coins). Very confusing stuff, granted. But you need to realize those things are only indirectly related to each other. They are
not the same. So, a Gold resource isn't the stuff you get from your tax income, and the coins that are displayed on the Gold resource aren't money you'll be getting to pay for maintenance or upkeep or upgrades or whatever.
These are separate concepts altogether. The first thing you need to understand is that the economy of the game is based upon the concept of "commerce" (looks like this:

). This represents all the economic activity, trade and transactions being made within your empire (and beyond, as there's also foreign trade routes). If you really think about it, your country (in real life) isn't taxing 100% of the entire economy, now is it? This is why there is the tax income stuff you've tried so hard to grasp in the past.
Tax income is the percentage of the total commerce going on in your empire that you choose to take out in order to pay for your government's expenses. This is real money, probably actual gold coins in actual treasure chests. Hard currency. It shouldn't bee too hard to differentiate between a farmer selling crops at the local market and getting paid in chickens

commerce

and the money

gold

your government officials are paying your soldiers for wages, equipment and supply. Because the grain farmer and the chicken farmer have both paid their taxes, which you then get in cash (not chicken!

).
So, that takes care of the commerce/tax issue. Now for the "special resources". If we forget about there being something as confusing as a Gold resource for a moment, we could take a look at another resource instead. Like Dye, which is also regarded a luxury item. Any special resource, like Dye (or Gold, but forget about that one for now), have double functions in a game of Civilization. First and foremost they are special resources, granting bonuses for health and/or happiness, or they enable you to build certain types of things - or give you discounts for building other things. You basically want them because you get bonuses from them, and having one is usually enough for all purposes. (Any additional ones you can trade away without losing any of the benefits associated with that resource.)
As for the Dye resource, this is a luxury resource and thus gives you happiness in all cities that have access to it. (Because your people all wanna live in the lap of luxury.) There is an additional happiness bonus for cities with the Theater building (as actors like to wear elaborate costumes, I presume). But, the actual tile where the Dye resource is located (on the map) will also get some bonuses.
You probably know (or at least should know) about the three types of yields cities can get from tiles. These are Hammers

hammers

, Food

food

and the afore mentioned Commerce

commerce

. Different tiles give you different yields - but only in the city that is working that tile! If no city is working a tile (like a tile that is beyond the reach of any city) there will be no yields from that tile -
whatsoever.
So, a tile containing a special resource gets bonus yields, and a tile containing Dye will give that tile some extra Commerce (
not gold or taxes or money or anything else). Because, when that dye is traded between the farmers who run the plantations and the dye grocers, and when the raw materials they sell are turned into actual dye, which then is bought by cloth manufacturers, who in turn sell their garments to consumers, Commerce is generated in your empire. Its not like the state treasury is getting all that dye or that all the proceeds from the production, selling and reselling of dye is taxed - only a
portion of it.
So, the Dye resource makes your people happy as they get to wear fancy dresses, but the business of producing and using dye is also growing your economy. The extra Commerce gained from that Dye tile is added to the city that is working that tile. Lets say that the city in question would have a total of 20 Commerce in yields every turn working that Dye tile. If your tax rate is 10% that means that the city will be paying your royal treasury 2 Gold

gold

in taxes every turn. Note that only a small portion of that

come from the Dye itself, but it does contribute towards it.
If you did manage to follow my thinking thus far, here's the flip: Substitute the Dye resource for a Gold resource (or a Silver resource, or any other luxury special resource) and it would work almost exactly the same! The only difference would be that a Theater wouldn't get you any extra happiness, but instead a Forge would (because that building will be used to melt that raw material into shiny things your populace will go bananas over). And there would be a different set of yields coming from a tile that has Dye than one that has Gold as a special resource. Also the additional bonus yields from Gold differ from those from Dye, and this is true for all resources. So, different resource, different yields - but only if a city is working that tile!
So, lets say, for the sake of argument, that a Gold special resource is within the reach of one of your cities. (You can see this by opening the City Screen - if you can't see the Gold - you can't work it either.) Since the tile in question is connected to your trade network you're already getting the happiness bonuses in your cities. Now, if you assign a citizen to work that tile (if one isn't already - the city governor can spot those things sometimes, you know) you will also get all the yields - base yields and bonus yields - from that tile. It would probably be some

, perhaps one

and a lot of

! But note that you never get any Gold from resources, even from the Gold resource. You get Commerce. Always Commerce! Because when you look at it you see

and not

. You know this to be true.
So, now all that Commerce is added to the rest of the Commerce produced by your city. Lets presume this is a rich commercial city so it has a total yield of 40 Commerce per turn. Your tax rate is still 10% (remember?), so the city will contribute with 4

to your treasury (not 4

as it will be converted into taxes, or

). Not as many

as it says on the tile, because the tile isn't promising you any

at all! Its merely suggesting you work that tile for the additional

, thats all.
Were you able to follow? Or do I need to put this into pictures?
edit: I posted a private message also, look for it under My Account in one of the menus above.