That's like asking what sense does it make for the WWE to elevate a champion that no one likes. Obviously the reason is to increase drama for when the good guy wins next time. (You'll note that the Spurs never won consecutive titles.)
The NBA isn't explicitly rigged. It's implicitly rigged by the superstar system, the galvanization of which is the defining feature of Stern's tenure. Stars get more calls, which makes them more successful, which makes them bigger stars, which gets them even more calls, which makes them even more successful, which ... you get the idea. That's not explicit, bent-corner envelope rigging, but more like, well, capitalism, in which the rich can use their power and their knowledge of the system to become richer, and the poor can never catch up without a major dose of luck.
Certainly, how much this implicit rigging defines the NBA is a question open to debate. But to say that having a team in lowly San Antonio win four titles proves that the system is fair -- no, the issue is rather subtler than that.