My main theory on this
Matt Bonner Phenomenon is two-fold, and comes from examining the 5-man-unit data on 82games.com:
1. The Power of Three Point Shooting
2. The Power of Balanced Lineups
Let's take a look at the top lineups in +/- last year:
-Parker-Mason-Finley-Bonner-Duncan: +88
-Parker-Mason-Finley-Bonner-Thomas: +48
-Parker-Mason-Ginobili-Bonner-Duncan: +28
-Parker-Ginobili-Bowen-Bonner-Duncan: +27
-Hill-Mason-Finley-Bonner-Duncan: +27
-Parker-Ginobili-Finley-Bonner-Duncan: +20
http://www.82games.com/0809/0809SAS2.HTM
Other than Matt Bonner, all of these lineups have 2 things in common:
1. They all have 3 players in the lineup who can hit the 3-pointer at a high percentage.
2. They are all balanced lineups with 2 big men, 2 swingmen, and 1 point guard.
The first part of this is purely offensive. By having 3 guys on the floor who can hit the three pointer, you open up the floor, and (assuming you're hitting your threes) you allow yourself to get more points per possession.
The second part of this has a lot to do with defense and rebounding. By having a balanced lineup on the floor, particularly the presence of two big men, you improve your defense and hit the boards harder.
So why do these two benefit Matt Bonner the most? Specifically, I think Matt Bonner is pretty much the only player on the team who never has to play in an unbalanced lineup. By having Bonner be the only big man on the court, you would basically be going to super small ball, and would theoretically give up a lot on defense; so, understandably, Pop has never gone to this lineup.
I'm not saying this is completely the reason, and it's just a theory. Nor is this a condemnation of small ball, though the numbers may be trying to show that (the worst +/- group last year was Parker-Mason-Ginobili-Bowen-Duncan at -29).
As a final note, you have to give credit to Bonner for his outstanding shooting and improving defense last year. Without his individual effort, all of this theory would be moot from the start.