I have been visiting South Africa regularly from 1989. Was there this year and last. Overall: I have never had a problem, many have. Daylight and transport that is known to those who know you works well.
When I have to go from JNB to Pretoria, my sister books me on a pre-booked car service. I get emailed with the details of the car type, colour and the name of the person who will meet me. Works every time. Always punctual and safe drivers. I get met as I emerge from baggage.customs and get delivered back in good time. Your journey from JNB to the Rovos Main Station in Pretoria means that you go nowhere near JNB city. The airport is out to the east of the city and Pretoria is to the north
If you are using more then JNB, let me know here on in PM.