Mercantilism as a trade theory is different from what we know of today as Capitalism (or the Free Market) in that rather than specialization of trade, it promoted the idea that the Empire should be self sufficient and own all of the resources it consumes. This economic concept is what drove Colonialism as a geopolitical foce during the age of colonialism and it is mercantile ideals that created and settled the new world.
The Civilization games, especially III and IV (featuring resources), tend to promote Mercantilist ideals more than free trade. It simply pays more to own the resources as they will never be under threat of being cut off.