The reason he's not getting minutes now is because there are better options now, i.e. Diaw, Splitter, and apparently Blair for the time being. That still doesn't mean he was bad on defense when Pop played him even when he wasn't hitting his shots.
Jose, I think you've generalized Bonner on the court. In other words, in your mind you've compiled the times that maybe Bonner did need help which resulted in the other team getting an easy score (because that is what most people seem to remember about him) and have concluded that that is his norm. It just isn't. If Bonner were guarding Lamarcus Aldridge or even Dwight Howard, then heck yeah they're going to send help. Even Duncan gets help. But in reality, the Spurs defense has never been about man to man defense anyway, it's always been about help defense. Bowen got help all the time, Duncan even in his prime as well.