Position a rack in the center of the oven and heat the oven to 350°F. Season the fish generously with salt and pepper on both sides. Coat with 2 tsp of the oil and set aside.
Heat the remaining 2 tbs oil in a 7- to 8-quart Dutch oven or other heavy-duty pot over medium-high heat. Add the peppers, onion, and garlic. Season with 1/2 tsp salt, and cook, stirring occasionally, until the onion is translucent and the peppers have begun to soften, about 5 minutes.
Add the canned tomatoes with their juice, wine, bay leaves, and 1 cup water. Bring to a boil. Lower the heat and simmer until the liquid has reduced slightly and the peppers are tender, about 10 minutes. Add the cherry tomatoes and cook until they soften slightly, about 2 minutes. Season to taste with salt and pepper. Carefully place the fish fillets in the pot, skin side up, and spoon some of the peppers, onions, and sauce over them.
Transfer to the oven and cook uncovered until the fish is cooked through, about 25 minutes. Serve topped with the parsley or thyme, if using.