It's a tiny country (population 2.3 million, vs South Africa's 60 million), mono-ethnic, rich in diamonds, strong culture of law and order.

South Africa also props Botswana up via a customs union.

https://www.tralac.org/news/article/6931-surge-in-botswana-s...

Competent forward-looking leadership.

There's plenty of factors that helped, I can think of a dozen right off the top of my head, but the one that made a crucial difference is in my opinion really the above.

Basically this: https://en.wikipedia.org/wiki/Seretse_Khama#Presidency