"The surname Khan, originated in Mongolia in Central Asia, used as a reverential title by a sovereign or military ruler, who ruled over a Khanate, representing an area of land and the tribes living therein. It was used by several Mongolian emperors who were mainly Shamanist and Buddhist in their beliefs including Genghis Khan and Kublai Khan. It can have one of several connotations, all related in some capacity to the title of Khan which originated from the Mongol Empire and its subjects and was thereafter historically granted to Muslim rulers. Infiltration of the name from Central Asia into South Asia happened with the coming of the various Muslim Turks, Afghans, and Mughals into South Asia who used this name as a title as well as a suffix to indicate their ethnic identity."
Both you and Alma are correct in your comments and I was aware of the Mongolian origin (Ghengis and Kubla, obviously). But more often than not these days when you see the name it seems to have a Pakistani or an Indian Muslim attached to it.