Preheat oven to 400°F. Line a baking sheet with parchment paper and lightly coat the paper with nonstick spray; set aside.
Place the flour, egg, and cornmeal in separate shallow dishes. Season both the flour and the cornmeal with salt and pepper. One at a time, dredge the flounder fillets in the flour, then in the egg, then in the cornmeal to coat. Arrange fish on prepared baking sheet and chill while preparing the salsa.
In a medium bowl, stir together the tomatoes, red onion, lime peel, and lime juice. Season to taste with additional salt and pepper.
Remove fish from the refrigerator and lightly coat with cooking spray. Bake for 12 to 15 minutes or until fish flakes easily when tested with a fork. Serve fish with salsa.