Position a rack in the center of your oven and preheat to 400°F (205°C). Line a large, rimmed baking sheet with parchment paper.
Pat the salmon fillets completely dry with paper towels. Rub all over with 1 tablespoon of olive oil and season generously with Kosher salt and black pepper.
In a medium bowl, combine the halved cherry tomatoes, sliced garlic, sliced shallot, the remaining 1 tablespoon of olive oil, optional red pepper flakes, and about half of the torn basil leaves. Toss to combine.
Arrange the seasoned salmon fillets on the prepared baking sheet, leaving space between them. Spoon the tomato mixture over and around the salmon.
Bake for 15-20 minutes, or until the salmon is opaque and flakes easily with a fork (an internal temperature of 125-130°F is ideal for medium-rare). The tomatoes should be soft and bursting.
Remove from the oven and let rest for 3-5 minutes. Garnish with the remaining fresh basil leaves before serving.
Notes
For best results, use an instant-read thermometer to check for doneness. Pull the salmon from the oven at 125-130°F for perfectly moist results.