In some aspects, yes, but in others, no. There was a case of xenophobia a while ago, but it was never targeted at Americans or tourists, more at people from other close African countries like Zimbabwe, and this was only due to the fact that, since the unemployment rate is rather high, some of the local people with low incomes felt threatened by the people crossing the borders illegally. They felt they were "stealing their job oppertunities". But that has been resolved quite a while ago.
And yes, there are many poor people, but middle-class and wealthy people as well.
The crime rate is high, granted, but it's not as unlivable the article makes it sound like. If you don't go around waving money in the air, showing off fancy jewelry or cellphones in public, walking alone at night in the streets, and you know which places to avoid, you should be fine. Some places are more dangerous than others, and you should avoid those places. I'd also say the best way to stay safe is to be alert, and to protect yourself with the use of locks, household-alarms, etc., and to know the basic safety rules that you'd use in any country (avoid strangers, don't leave little children unattended, draw attention to yourself if someone is threatening your personal space, etc.)
I've lived in South Africa my whole life, in various regions.