In 4-quart saucepan, heat 1 tablespoon of the oil over medium heat. Add onions, 1/8 teaspoon of the salt and the red pepper flakes; cook 6 to 7 minutes, stirring occasionally, until onions are softened and lightly browned. Add quinoa; cook over medium heat 1 to 2 minutes, stirring occasionally, until fragrant. Add tomatoes and water. Heat to simmering over high heat, stirring occasionally. Cover; reduce heat to low. Cook 18 to 23 minutes, stirring once, until liquid is absorbed and quinoa is thoroughly cooked. Remove from heat; stir in 1/4 cup of the cheese.