Heat oven to 400° F. In a roasting pan, toss the fennel, onion, garlic, tomatoes, thyme, ½ teaspoon of the salt, ¼ teaspoon of the pepper, and the oil. Roast for 20 minutes.
Move the vegetables to the sides of the pan; place the salmon in the center. Squeeze the lemon halves over the salmon. Sprinkle with the remaining salt and pepper.
Return the salmon to oven and roast until it is the same color throughout and flakes easily, 10 to 12 minutes. Serve with the rice, if desired.