I do see what you mean. Just trying to make sense of the way Civ deals with it.
I think the "Foreign Trade Routes" in Civ represents imports, or rather a tax by your city on imports.
When you adopt Free Trade as a Civic, dont you get extra foreign trade? "Free Trade" in real life went against mercantilism (I think) by encouraging imports over exports. Civ represents this by giving you extra foreign trade. I reason then that the foreign trade coins you get are your taxes on the imports.
Seen this way (foreign trade route coins as import taxes) mercantilism and free trade civics make sense.....or do they? May be straining to circle the square here.
Oh - and may be mixing up my coins and gold also. Not at my home PC so cannot recall for sure whether you get coins (ie

hard cash) or commerce (

that is then turned in to gold/beakers/culture/spying according to the sliders).