I wouldn't say that Johannesburg is more dangerous than other big cities around the world, especially if you don't venture into areas that are specifically unsafe. I've lived in Pretoria and Johannesburg my whole life (except 1 year) and I've never been the victim of a crime. The people I know who've been victims of crime did things like leave valuables lying around, they didn't lock doors when they should have or they were in places that are specifically unsafe. The safety issue is often sensationalized and exaggerated by the media and sometimes expats. If you stay in an area like Sandton or Rosebank, take the Gautrain to Park Station and do the City Sightseeing tour with the Soweto extension or a different organized tour the chances are low that anything bad will happen.
In my opinion Johannesburg isn't the most interesting place in SA though and I would recommend it if you like cities/urban landscapes and are interested in history. Other things you can do is visit the Drakensberg for hiking and stunning scenery, do a Sani Pass day tour to Lesotho, fly to George and visit Knysna with its lagoon and indigenous forests, fly to Port Elizabeth and visit some places on the Wild Coast. Durban is an option (it's not necessarily safer than Joburg though) and is interesting because of the Indian influence and there are some nice beaches in towns around it. You can also consider St Lucia and the iSimangaliso Park.
I hope this helps! :-)
