Towards the end of the war in the pacific, some Japanese submarines were used to deliver supplies to some outposts because the U.S. anti-commerce submarine effort had made it pretty much impossible so do so with surface ships.
Source: I think Morrison said it in Two Ocean War, I can try to look up the page tomorrow if you really want.

They weren't true submarines (the superstructure remained above water at all times), but the Whalebacks used on the Great Lakes at the turn of the 20th century come to mind. These vessels, built to haul coal, grain, iron ore, and other bulk materials around the Great Lakes (and serving alongside more traditional Great Lakes Steamers like the Howard Shaw) were designed with rounded tops (without gunwhales), bows and sterns. When carrying a full load, they rode very low in the water, allowing waves to simply wash over the top of the deck rather than crash into the sides.

Submarines are not efficient modes of cargo transportation. Legal commercial operations stand nothing to gain from their use. Depending on your view of the term "commercial" submarines have been used to transport illegal drugs :http://mobile.nytimes.com/2012/09/10/world/americas/drug-smugglers-pose-underwater-challenge-in-caribbean.html.

I cannot , however, definitively say submarines have never been used in legal commercial ventures. There's always the possibility of an outlier incidet.

Hey there! I wrote briefly on such a submarine that saw service as a merchant vessel in World War One: the Deutschland.

Two unarmed germans submarines were used to trade with the US ( when it was still neutral ) in WW1, they only made a few trip and were then fitted with torpedo tubes and deck gun.

If you want detailed information check out http://www.fas.org/man/eprint/german-subs.pdf starting at page 15.