short answer: b'se it was the only part of Africa with a non-sedentary, non-complex society that was -compared to the other interior societies- relatively easier to subdue

the khoi and san were quite fierce fighters but compared to the interior states with a long history of warfare, these two groups couldn't sustain a large scale conflict for long; as was the case in the dutch-khoisan wars of the 17th century

to be technically accurate, it was only the cape colony and not south africa as a whole that was subjected to european settler colonialism and the reason was mostly because african armies that europeans encountered elsewhere where at this time, too strong for the europeans to defeat (unlike the 19th century) and these defeats were total and decisive for example the battle of kitombo involved as many as 400 Portuguese soldiers and more than 10,000 auxiliaries which was almost as many as the 19th century colonial armies of 1,000 or so Europeans and 5,000 or so African auxiliaries eg during the first anglo asante wars

Europeans' initial attempt at colonizing Africa ended after a series of humiliating military defeats. this attempt was mostly led by the Portuguese who first faced off with the sene-gambian archers in the 1450s (these same archers also rebuffed an english raid on the sene-gambian coast in the 17th century), second were the Portuguese wars in the west-central african kingdoms of kongo, matamba and ndongo between the late 16th and mid 17th century that included queen njinga's wars with the Portuguese (and the latter's expulsion from matamba), and ultimately, the last major afro-euopean war of this period in west-central africa which ended with with portugal's defeat by kongo's province of soyo in 1670's battle of kitombo (it would take another 200 years for a Portuguese military expedition into the angolan interior),next was mutapa and changamire's wars with portugal that ended with Portugal's explusion from the interior of zimbabwe in the 1690s where he razed several Portuguese towns in their vassal of mutapa, the latter soon uprooted all Portuguese settlements by the 1710s, the last major Portuguese loss was along the east african coast where the Portuguese were defeated by an omani-swahili coalition in their final stronghold of mombasa in mombasa when they lost fort jesus in 1698, the Portuguese were thus relegated to a small coastal strip along the mozambique and angolan coasts plus a narrow stretch of land a few miles inland along the kwanza river of angola and thezambezi river of mozambique

john thornton has covered these afro-european wars in: "Warfare in Atlantic Africa, 1500-1800" , and his others articles such as "Early Kongo-Portuguese Relations: A New Interpretation" and The Kingdom of Kongo and the Thirty Years' war" on the swahili, omani, portuguse wars read: "Navigating the Early Modern World: Swahili Polities and the Continental-Oceanic Interface" by Jeremy Prestholdt