One thought was to quilt around the inside edge of the flower clusters. You could also quilt inside the center hexagon of each flower if you needed additional stitching to secure your batting.
The most time consuming method, but my favorite, would be to quilt inside each hexagon. You could do multiple hexagons without tying off your thread by moving the thread from hexagon to another inside the quilt.
This one looks a little strange in the diagram, but I think it would be very interesting on a quilt. It feels a little modern to me.
This one looks peculiar in the diagram too, but I think it would actually work well. A major advantage of going with diagonal stitching is that you avoid the bulk in the corners of the hexagon by stitching only through the straight sides.
Added on 4/27/10. Kait had a great suggestion and I think this is close to what she described. Another great choice!
I know there are many more options for quilting patterns and I would love to hear your suggestions. What other interesting ways have you seen to quilt a hexagon quilt? Do you have a vintage grandmother's flower garden quilt that has interesting quilting?