Preheat oven to 350°.
Place beans, 2 tablespoons lime juice, cumin, and garlic in a blender; process until smooth, scraping bottom and sides frequently.
Combine tomatoes, cilantro, vinegar, jalapeño, 1 tablespoon lime juice, and salt. Toss and set aside.
Place a large nonstick skillet coated with cooking spray over medium-high heat. Add bell pepper and onion; coat with cooking spray and cook 4 minutes or until onion is crisp-tender.
Place tortillas on ungreased baking sheets. Spread equal amounts of bean mixture on each tortilla. Add onion and pepper mixture evenly to each; top with cheese, and bake at 350° for 5 minutes or until cheese melts. Remove from oven; sprinkle evenly with tomato mixture.