I am not a great fan of organised tours, I don't like being held to strict schedules, nor am I a great fan of being stuck with the same travellers for the duration of my holiday. You are also, often. at the mercy of the tour guide as to what you end up seeing, although some may give you options.
However, there are also exceptions to the rule and South Africa is a prime example. Unfortuntely it is a sad reality that there are security concerns in the country and there are definitely "no go" routes and areas, even in the big cities.
By travelling with a reputable tour company you will be able to explore this beautiful country, whilst at the same time, remaining as safe as possible.