I lived for 6 months in South Africa ( cape town) and did some work for a charity magazine, using mixes of a 30D and a 5D, never really had much of a problem, a couple of dodgy looks every now and then (especially in the townships) but nothing to really shout home about.
A few tips I got from a journalist friend of mine (whos worked in SA for 20 years)
1) Put a crappy strap on it, No Branded straps.
2) Put gaffer tape over the logos.
3) put tape on the grip, for some reason cameras are less likely to be stolen if they have a dodgy looking grip.
4) Insurance is a must and never fight. God for bid something does happen just let it go.
5) Use loads of memory cards. Use them like film take 25-50 shots then change the card, if your camera gets stolen you will only lose a few shots.
6) have a good bag, which is definitely not a camera bag! But is easy to get the camera out and back in again, last thing you want to do is stand there and struggle to get it in or out, draws attention.
7) look like you know what your doing, try to look like you've done this all before, reduces the tourist look.
Lastly a quick fact, last year more tourists were mugged in Rome, London and the costa brava than in SA.