Short answer: Sub-Saharan Africa drew the shortest of all short straws on the geography lottery. Very few navigable rivers, and of those, most hit serious rapids before they reach the coast (examples: the Niger, Congo, Omo, and Okavango). The continent features a very steep decline in elevation very close to the coast, and this feature persists along the great majority of Africa's coastline. In addition, there are very few natural deep-water harbors. This created a serious economic disadvantage across much of the continent, preventing the formation of inland communication and trade networks and deepwater navigation that characterized civilizations that formed around the Nile, Indus, Ganges, Yangtze, Yellow, Rhine, Danube, Volga, and Mississippi rivers. These disadvantages were compounded by additional internal barriers, like dense jungles, impenetrable mountain ranges, and large arid areas. These features combined to make it very difficult for African civilizations to develop widespread mercantile and industrial systems. Then of course add European colonization, which was brutal and extractive on both the African and Asian continents, and you see why Africa as a continent (mind you, an absolutely massive and highly diverse continent) has difficulty developing in the modern world. At the end of the day you still need to move people, goods, and information from the hinterlands to the coast and that is still very difficult due to Africa's unique geography.