This sounds like a potentially 'hot' subject! Or maybe too big a scope for most people to take on board... Having learnt to fly in Africa, and am still flying commercially in the region, I think the safety issue comes down to a few key points.
Like ageing equipment which appears in a previous post. Aircraft/radios/nav aids that have been 'thrown' out by the West are frequently found operating happily in Africa. I recently got shown around an Antonov that still had bullet wounds from the PREVIOUS Afghan war in its fuselage!
Then there's the training. Personal experience of local training is that it is more important to have a uniform and tie, than quality instructors. Its more important for flying schools to churn out commercial pilots in quantity, than try to achieve quality. People in flying schools are often on a limited budget, and certificates are more important than practical flying skills. 250 CPL with gas turbine/C208 on licence with no idea what keeps a plane in the air or how to really fly. Schools that are so concerned about their accident records, they OFFICIALLY send out students on solos with safety pilots on board, and forbid them to land away from base airports in case of problems.
And lastly the reason a majority of pilots take up flying as a career - its not because they are passionate about flying, and spend all their days dreaming of being in the air, watching birds fly and wind effects etc. No, its often seen as a career that gets you out of Africa, paid opportunities to settle in the West, supply families and relatives with Western goods etc. Most jobs are seen as a fast track to an airline job, where decisions are taken from you and you always fly with a co-pilot. Nice and safe. But not passionate.
I also believe that the more automation there is on board the less pilots have to think for themselves, and the less they can think for themselves when things go wrong and the automation lets you down. I don't think Africa does itself any favours with its no-blame policy either. If someone has a mishap lets all learn from their experience - but no, culturally we'd rather bury the whole story or make a hero out of the guy who screwed up rather than admit we're human and flawed.
We still have way too many CFITS despite GPS, we're still trying to be heroes and land in marginal conditions, we still don't admit we're not as good as we should be, if the job demands it we'll fly a bucket of bolts than be principled adn say its unairworthy, we'd rather blame a hitherto unknown weather/mechanical issue than confess we let things get out of hand, and its more important to look the part and have the paperwork than to be actually able to do the job. Fly solo in the bush - NO, our families would much rather we were soft & comfortable in an airline job for all the goodies that go with it.
There are pilots in Africa that are skilled, principled, talented, trained and fit for the job in great aircraft, doing an amazing job. There are also too many that aren't.