The factor most to blame is geography. As necessity is the mother of invention; human beings, civilizations and societies are ultimately shaped by their surroundings and how they interact with them. The African continent compared with Eurasia or the America's is undeniably one of the most harshest landmasses (ecologically speaking) in the world. In Africa, human beings have to face of against the aridity of the Sahel, dryness of the Sahara and the humidity and malaria of the tropical interior (around the equator). Only Antarctica, Northern Eurasia and Australia are considered more inhospitable for human habitation compared to it. As a result, establishing stratified communities on the African continent proved more difficult, but not impossible (Mali Empire, Ethiopia, Somalia etcetera). Another factor why human beings in Africa weren't able to develop to the degree of their Eurasian counterparts is also the difficulty in communication. In Europe, travel was relatively easy compared with other parts of the globe due to relative size and also because of rivers such as the Danube, Rhine, Volga, Dnieper, Tiber and the Seine (to name a few) which acted as thoroughfares.
Rivers provide not only a source for agricultural nourishment but also act as natural "roads" for people to travel along and as landmarks to aid in getting ones bearings. Also the Mediterranean, has been considered the cradle of many civilizations such as the Phoenicians, Greeks, Romans and so-on, and because of this you basically have a cross-cultural melting pot; a collective lake from which everyone can travel and transmit information, innovations and ideas back and forth. If you add the temperate climate, lush vegetation and fertile soil of the European Continent; theirs pretty much little other reason as to why Europe came to dominate the globe. In Africa however, the only the parts of the continent to benefit from geographic arrangement the Classical era were those lands straddling the Mediterranean, as well as lands connected by the Nile river (Kush, Aksum, Meroë) and along its most major estuaries (Abyssinia). The societies along the western part of Africa such as the Ghana, Mali and Songhai empires only flourished due to the domestication of the camel; which allowed the to traverse the Sahara with greater ease and thus establish links with coastal Mediterranean centers such as Carthage & Cyrene.
When establishing the reasons behind the relative primitiveness of African societies further south of the equator, the conditions behind them can be attributed mostly to the lack of a direct communication-link between the northern and southern parts of the continent. In antiquity, peoples along extreme south-western part of the continent (such as Khoikhoi and the San aka. "Bushmen") developed very differently in cultural and linguistic terms compared to their neighbours (the Bantu) due not only to their isolated environs, but also the ability in which they could interact with their northern part of the continent (e.g. trade winds). To summarize; geographical constraints and isolation have a tendency to extremely stunt development of human societies and in some cases lead to their eradication (e.g. Amerindians). To state one last interesting example, the Australian Aboriginals had lived the same cyclical hunter-gatherer lifestyle for over 40,000 years. They were so isolated from the rest of the world that they didn't even receive the know-how to develop the bow and arrow. It was only when the European settlers arrived that their long established archaic lifestyle was irreparably disrupted, and hence they were sadly brought very close to extinction.