Heat a broiler or grill to medium. Broil or grill the flatbreads 4 to 5 inches from the heat until lightly toasted, 3 to 4 minutes per side.
Spread the pesto over the bubbly side of the flatbreads. Scatter on the tomato, pine nuts, cheese, and pepper flakes (if using).
Return the pizzas to the broiler or grill and cook (with the lid down over low heat if grilling) until the cheese begins to melt and the pizzas are crisp, 4 to 6 minutes.
Tip: To seed a tomato, cut it in half crosswise, hold each half upside down, and gently squeeze it while digging out the seeds and gel with a knife or your fingers. Having trouble finding naan style flatbread? Flatbread is available by special request at your local Panera Bread bakery-cafe.