The only purpose of monopolies is to give your merchants traits, they can get up to +3 skill, which will get them a lot more money. To gain the traits your merchants just needs to sit on a resource that there are multiples of in a single region, e.g. amber in many northern europe areas, silk and spices in several areas of middle east and many many more. If another faction's merchants are on the other spot in that region you won't get the traits.

The way I use monopolies is have my merchant sit on them for maybe 10 turns to gain a couple traits before they trek halfway across the globe to the really profitable areas. Sending a new merchant with 1 skill to the middle east is asking for him to be "acquisitioned". On the other hand, I have never sent merchants to Timbuktu, but I guess people like it because you get huge money and there is no competition so you don't have to worry about sending a newbie merchant.