At the moment, there are only a few thousand U.S. troops in Africa. Most of them are Special Forces or military trainers. There are Islamic terrorists operating in Somalia, and to the west in the semi-desert Sahel region, that goes all the way to the Atlantic ocean. There are also several fragile nations, threatened more by internal disorder than Islamic radicals, although Islamic terrorists can be found everywhere on the continent. It makes sense to form a new command just for Africa, even though northern Africa is more a part (culturally) of the Middle East. Setting up the African Command would deprive the European Command of most of its work. For decades, the European Command was "the" Command, as it controlled the forces facing the huge Soviet armies to the east. But since the end of the Cold War, all the European Command has had to deal with is the Balkans, and, increasingly, Africa.
The U.S. Department of Defense is planning to set up a separate command for Africa. The Department of Defense has five military commands to take care of U.S. military operations in different parts of the work. Currently, responsibility for Africa is divided between three of the five commands. Thus the European Command controls operations in the 43 countries of North and sub-Saharan Africa. Central Command deals with the Horn of Africa; and Pacific Command looks after the island of Madagascar, off the east coast of Africa.