This makes sense. Duncan is still by far the Spurs best defender (best big man) and pairing the weakest of the 4 with him only makes sense at this point. It makes 0 sense to start Tim/Tiago when your backups or 2nd unit will consist of Bonner/Blair. Saying that, Blair is still getting too many minutes and Tiago needs to take those. At the end of the day another big man is needed.
On another note, Bonner has played well all year long and the people hating on him will never stop. His defensive #s this year have been fantastic but the haters refuse to acknowledge them. When the Spurs struggle he will always be a scape goat.