Wash hands with soap and water.
Preheat oven to 400°F.
Gently rub fresh tomatoes under cold running water.
In a bowl, toss the tomatoes, 1/4 cup of olive oil, salt and pepper. Place mixture on a baking sheet and roast for 45 minutes.
Scrub onion with a clean vegetable brush under running water. Gently rub fresh garlic under cold running water. Chop the onion and mince the garlic.
Place a large stock pot over medium heat. Add the onions, garlic, red pepper flakes, the remaining 2 tablespoons of olive oil, and the butter. Sauté for 10 minutes.
Add the canned tomatoes, basil, thyme, chicken stock, and oven roasted tomatoes (including the liquid on the baking sheet).
Bring to a boil. Lower heat and simmer uncovered for 40 minutes.
Pass tomato soup through a food mill with the coarsest blade.
When reheating leftover soup, reheat it until internal temperature reaches 165 °F on a food thermometer.