PE is safe
There is hardly a safer place in South Africa than Port Elizabeth. Violent crime is negligible and is no more prevalent than in any similiar city in the USA or the UK!! Petty crime is quite rampant but is mainly limited to theft of a non-violant nature.
If you are looking for good value training, then forget about 43 Air School and look at APTRAC or the Algoa Flying Club in PE. It is a fantastic city with lots to do when you are not busy with flight training. Great beaches, restaurants, night clubs, friendly people and fantastic recreatonal activities (game farms etc) within a couple of hours drive away.
The only major negative with training at any of the coastal schools is the wind and weather which will see you wasting at least a third or more of your time waiting it out.