We got the Shosholoza Meyl train from Johannesburg to Cape Town, which was a brilliant experience, loads cheaper and more interesting than flying. It was much easier than expected, and although we were worried about Park Station acually it was totally fine.
If you are travelling between the airport, Pretoria or Johannesburg the Gautrain is totally safe.
If you're staying for a while and plan on visiting lots of National Parks it's worth getting a Wild Card from SAN Parks (check their website).
Good luck, hope you enjoy it