I think you're merely using the wrong statistical measure.
Plus-Minus is heavily reliant on who else was on the floor with him. If he happened to share the floor mostly with Duncan/TP/Manu, then he would look great. If he happened to share the floor with Mason/Finley/Vaughn then he would look horrible.
One could use PER, and then he would rank as an average NBA player (15.0).
PER, IMO, actually works well in his case, since the main knock on PER is that it largely measures offensive performance, and we know Bonner is nowhere near an elite defender (PER was largely unfair with players like Bowen, for example).