My experience of African aviation is limited (but I do have some!), so I am sure there are others who are better qualified to answer but here's my two cents anyway!
Acting in their favour:
- Some very good stick and rudder pilots.
- A genuine commitment and passion from most in the aviation sector.
Acting against African aviation safety:
- Old aircraft.
- A relatively cavalier (or even cowboy) attitude of some operators. This is fostered by the African spirit of adventure and left unchecked by some authorities. Many authorities have realized this and are now playing catchup on their own limited resources.
- Old aircraft.
- Old equipment in general. For example not many navaids or approach aids. Many not maintained to the standards of the developed world.
- Inadequate supply of well trained people leading to many 200 hr people flying with relatively little supervision. The same goes for ATC and engineers.
- The geographic problems imposed by Africa. It's so vast and spread out that if anything happens help is so far away.
- The meteorological problems. In the developed world you're surprised if you can't get a TAF / METAR for where you're going. In Africa it's a luxury. Add to that the extreme weather which can build very quickly and you're in trouble.
So... is aviation in Africa really unsafe? Statistically you're more likely to die in a plane in Africa than in Europe or America. But you're also more likely to die in a car. Does that make driving unsafe? It's a question of how much risk you're willing to take. These risks can be mitigated by flying with reputable operators. IMHO, these flights present an acceptable level of risk.