Preheat oven to 425 degrees F.
Lightly oil a large shallow baking pan with 1 tablespoon olive oil.
Arrange peppers, cut sides up, in baking pan, and lightly oil the cut edges and stems.
In a bowl, toss the tomatoes, onion, basil, garlic, 2 tablespoons oil, red pepper flakes, mozzarella, and salt and pepper, to taste.
Divide mixture among peppers and roast in upper third of oven until peppers are tender, about 20 minutes.