In large resealable food-storage plastic bag, mix cheeses and flour. Seal bag and shake until cheese is coated with flour. In fondue pot, heat broth and milk just to a simmer over warm/simmer setting (do not boil).
Add cheese mixture, about 1 cup at a time, stirring constantly with wire whisk until melted. Cook over warm/simmer setting, stirring constantly, until slightly thickened. Stir in tomatoes and onions.
Keep fondue warm over warm/simmer setting. Serve with breadsticks, pretzels and vegetables for dipping.