This is from Africa"s Aviation forum so I think it should be reliable, these are 2006 numbers.
http://africaspotter.6.forumer.com/viewtopic.php?t=800
1... Johannesburg 16,266,706... 11.1%
2... Cairo 10,249,907... 3.7%
3... Cape Town 6,914,353... 9.8%
4... Sharm el Sheikh 4,793,652... -2.4%
5... Casablanca 4,625,908... 14.5%
6... Hurghada 4,584,847... -1.5%
7... Nairobi 4,376,667... 9.4%
8... Monastir 4,114,390... 8.8%
9... Lagos 3,794,964... -1.0%
10. Durban 3,764,480... 14.9%
11. Tunis 3,705,549... 4.9%
12. Algiers 3,464,741... 2.5%
13. Jerba 2,416,597... 2.9%
14. Marrakech 2,358,817... 24.6%
15. Mauritius 2,175,376... 3.9%
16. Luxor 2,047,822... -10.9%
17. Abuja 1,985,142... -9.1%
18. Addis Ababa 1,962,012... 14.8%
19. St Denis 1,474,269... -7.2%
20. Port Elizabeth 1,326,109... 16.9%
21. Agadir 1,263,286... 1.5%
22. Dar es Salaam 1,142,359... 7.5%
23. Mombasa 1,119,135... 7.6%
24. Luanda 1,010,351... 35.7%
25. Port Harcourt 989,977... 19.8%