South Africa has a lot of problems, including the rape and violent crime rate, an immigration and emigration problem, and a whole bunch of other issues. The problem is that South Africa, despite its problems, is possibly the only country seriously in the running. Only a few countries in Africa have the necessary airport infrastructure to handle international visitors at this scale, as well as the necessary economy needed to keep the infrastructure for the cup going. South Africa is one, and Egypt is basically the other (some noise about Morocco here).

I think putting the Cup in Egypt would have made it more of an Arab-Mediterranean affair, whereas South Africa was probably the only choice in sub-Saharan Africa. They're by no means perfect, but I don't think they can keep ignoring Africa when they choose sites for the Cup, so this was probably considered a decent compromise.