UPDATE The formula has changed as of the March 2011 patch, it is now
(city population * 1.1) + (capital population * .15) - 1 for each city connected to the capital, not including the capital.
- The Machu Pichu wonder increases the modifier by 20%, to
(city population * 1.3) + (capital population * .15) - 1.
- Arabia increases the constant by 1, to
(city population * 1.1) + (capital population * .15) (thanks WillfulWizard).
The economic overview also gives a far better explanation of how it is calculated - in other words, this question is now trivially solved by simply looking at that economic overview :)
Original answer below.
Okay, I did a bit more testing, and bwarner's answer is almost accurate:
Each city, excluding the capital, provides (city's population * 1.25) + 0.01 gold per turn. Owning the Machu Pichu wonder increases the modifier by 20%, to (population * 1.5) + 0.01, for all the cities.
The capital does not provide any gold.
The 1.25 and 0.01 can be seen in the Assets\Gameplay\XML\GlobalDefines.xml file:
<Row Name="TRADE_ROUTE_BASE_GOLD">
<Value>1</Value>
</Row>
<Row Name="TRADE_ROUTE_CAPITAL_POP_GOLD_MULTIPLIER">
<Value>0</Value>
</Row>
<Row Name="TRADE_ROUTE_CITY_POP_GOLD_MULTIPLIER">
<Value>125</Value>
</Row>
The economic overview also demonstrates these values.
I couldn't find any other factor which affects these values, and I checked different difficulty levels, different distances between cities, different city route type (road vs railroad, road/railroad vs harbor), different city health and whether it is occupied. Looks like it's solely the population.
I recommend not "investing" in a city-state unless you can get some influence for free to start out. Killing Barbarians or doing another quest for them will get your foot in the door, and let the $250 you have to spend periodically give you a lot more value. For instance, that $250 will be keeping you above the "Allied" line instead of just barely making you friends with the city-state.
Likewise, as mentioned above, the Patronage tree will give you significant bonuses to your influence over city-states.
It seems that the design is such that in the early game you won't be able to guarantee a city-state ally without committing a lot of cash.
To elaborate (not 100% sure on all these numbers but the overall point is still valid):
If you spend $250 to become Friends with a city-state, starting from 0 influence, you'll get 35 influence, making you barely Friends (30 influence). This means you'll be friends for 5 turns, at which point you'll need to spend another $250 to be friends again. You probably don't have another $250 that soon, though, so the influence runs all the way down close to zero before you're able to spend another $250, which again only gives you a few turns of friendship. This is obviously unsustainable.
If instead you perform a mission for the city-state and get 30 or 40 influence to start with, every time you spend $250 you'll get to use all 35 points of that influence before needing to spend another $250.
Similarly, you'd be better off saving your money to start with $500 worth of influence than buying $250 and not being able to afford more right away.
Long story short: if you're already friends, you get more value for your money. Likewise, if you're already allies, you get even MORE value for money you spend to sustain at that level.
Best Answer
If your harbor is connected via railroad to your capital, the harbor connection counts as a railroad. You'll have then to lay railroads from your harbor on the other continent to any inland cities.
In the following example B,C and D would receive the bonus, E would not.
In the next example no city would receive the railroad bonus.
As DMA57361 pointed out, if the capital has a harbor, any other city with a harbor automatically receives the railroad bonus. In the next example, C and D receive the bonus, E does not.
Legend: