Preheat oven to 350 degrees F (175 degrees C). Lightly grease a 9x13-inch baking dish.
Heat oil in a large skillet over medium heat; cook and stir green pepper, onion, and garlic until tender, about 7 minutes. Stir in beans, tomatoes, picante sauce, chili powder, cumin, and red pepper flakes; bring to a boil. Reduce heat to low and simmer, uncovered, until heated through and mixture thickens, about 5 minutes. Fold in rice and 1 cup Cheddar cheese; cook until heated through, about 5 minutes.
Spoon a rounded 1/2 cup bean mixture down the center of each tortilla. Fold sides over filling and roll up. Place enchiladas seam side down in baking dish; spoon salsa over each tortilla. Cover baking dish with aluminum foil.
Bake in preheated oven for 25 minutes. Uncover and sprinkle with cilantro and 1/4 cup Cheddar cheese. Bake until cheese is melted, 2 to 3 minutes.
