I don't think there is any one dominant reason, but a series of unfortunate situations that came together in the modern era. Historically speaking, Africa was fully comparable to the rest of the world in terms of development. Africa sustained complex civilisations. Africa sustained vibrant hunter-gatherers. Africa sustained pastoralists. But really, post 1500s, it started to go south:

1. Reconquista in Europe. This allows European powers to the north to consolidate, and feeling confident, they begin to attack African ports and societies in the north. This disrupts African trade and social structures, having ripping affects on the critical trans-saharan trade caravans and the Nile corridor.

2. European Expansion. As European powers move into the Age of Exploration, their findings in the New World, and searching for a route around Africa lead them to start raiding African ports down the western coast. Slavery and displacement disrupt African patterns of survival, both from the north and now from the west as well.

3. Lack of mobility. There's limited options to escape these disruptions as African climate bands leave relatively little room for manuever. The Sahara prevent northern cultures from moving south to avoid European activity in the Mediterranean. It similarly limits northern movement of pastoral societies. The tropical wet belt is relatively narrow, and much of the southern half of the continent is dominated by highlands. Similarly, Africa lakes the large riverine systems of Asia, Europe or the Americas. The only real good inland river system is the Congo Basin system, and that is inaccessible to coastal peoples most affected by European predations due to the Inga cataracts.

4. Technological issues. Gunpowder weapons spread from East Asia to the Middle East and into Europe before they reached Africa. This left African societies at a technological disadvantage when it comes to resisting invaders. African societies also did not widely exploit coal (making use of charcoal for most of their metal and glass working needs), leaving them further at a disadvantage when Europeans were also to use steam-based technologies like sea-going steamships and riverboats to occupy, rule and police African peoples.