It is all about money.
Most of Africa is in serious poverty so funds for infrastructure and modern aircraft are simply not available. This feeds a culture of "make do and mend" and low expectations.
Unlike the first world airports capable of taking passenger jets are also a long way apart so when something goes wrong you are usually around 100 miles from the nearest NDB which stopped working years ago and has never been fixed and your nearest diversion is probably 250 miles away.
Pilots often come up through the GA and 19 seat market making a living as bush pilots. Most are excellent at their job but when they eventually make the transition to an airline they are deeply ingrained with the african aviation culture. This is not really compatible with best airline practice.
Airlines which cannot afford decent salaries attract less experienced crews who, in turn, have more interest in building enough hours to get out than in building a professional company culture.
It really does all come back to insufficient money and lack of investment.