Most of the military submarines listed so far weren't built as cargo subs -- most were converted minelayers or were built to carry fuel and ammo to seaplanes and other subs (which I suppose are technically cargo carriers, but not in the sense of carrying cargo from port to port (or port to beach). The WWI German Deuchland class was one exception and the Japanese Ha 101 class being another exception.
While these boats were poor cargo carriers (in terms of total weight devoted to cargo) they were also much stealthier than surface freighters.
And if a sub can carry cargo, it can carry troops -- the USS Argonaut being one example (after her minelaying gear was removed, she was one of two subs involved in th Makin Island raid and carried part of the 120 Marine force).
http://en.wikipedia.org/wiki/Ha-101_class_submarine
http://en.wikipedia.org/wiki/USS_Argonaut_(SM-1)