Botswana is not your average African country. It is modern and developed and most things work. You can safely drink the tap water in towns and cities and you don't need protection against cholera or yellow fever.
HIV/AIDS is a serious issue but, unless you fail to take common sense precautions, there should be no undue risk. In fact, the greatest danger to the traveller is caused by wildlife and the inherent risks of driving in the bush.
The most significant concern for independent travellers is road safety. Botswana has one of the highest accident rates in the world, and drunk and reckless driving are common. Cattle, goats, sheep, donkeys as well as wild animals are deadly hazards on the road, especially at dusk and after dark when visibility is poor. To drive in Botswana you need to be prepared for the unexpected and observe the speed limits on unsurfaced roads.