Most of the time I match the binding, but once in a while I use the thread that I used for the quilting if matching the binding isn't practical. Something my binding is made up from more than one fabric, or I use a large scale print and the binding ends up with a lot of different colors showing. Those are the times when I match the quilting thread.
One note, because of my method, the bottom thread is on the quilt, not the binding. In all cases, I use bottom thread that will blend in the best with the backing.