Place oxtails in a large bowl. Add sliced onion and soy sauce. Mix well. Refrigerate at least 2 hours.
Combine flour, salt and pepper. Dredge oxtails in mixture making sure all sides are covered. Reserve onion.
Heat oil in large Dutch oven until hot. Brown oxtails. Remove meat from pan, drain off all but 1-2 tablespoons oil. Add reserved onion, tomato, bell pepper, chili pepper and garlic to pan and saute lightly, scraping up brown bits. Add hot water and molasses and stir well. Return oxtails to pan and cook over low heat for 1-1/2 hours. Add thyme sprig and continue to cook 30 minutes longer.