In skillet, cook ground beef and onion till meat is brown and onion is tender; drain. Stir in beans, salt and pepper.
Place 1/3 cup meat mixture on each tortilla shell. Top with chopped tomato; roll tightly and place seam side down in a 9 x 13 baking dish.
Melt butter; stir in flour. Add milk and enchilada sauce, whisk till smooth. Cook and stir till boiling; boil for 1 minute. Stir in cheese till melted. Pour over tortillas. Bake in a 350° oven for 30 minutes.