Preheat the oven to 400 degrees F (200 C). In a large bowl, combine the tomato halves, 1/4 cup of olive oil, kosher salt, and pepper; toss to combine. Spread out the tomato halves on a rimmed baking sheet, and roast for about 35 minutes. Set aside. (This step can be done several hours in advance.)
In a Dutch oven or large stockpot over medium heat, warm the remaining 2 tablespoons olive oil. Add the onions to the pot and cook, stirring occasionally, until beginning to soften, about 5 minutes.
Add the garlic and red pepper flakes, and cook just until fragrant, about 1 minute more. Stir in the canned tomatoes, roasted tomatoes, basil, thyme, and chicken broth. Bring the entire mixture to a boil, then lower the heat and simmer, uncovered, for 40-50 minutes.
Use an immersion blender, standard blender, or food processor to puree the soup until smooth, and serve.