In a large resealable bag, combine salsa, lime juice, onion, garlic, bell peppers and flank steak. Seal and marinate in refrigerator at least 4 hours or overnight, turning occasionally.
Prepare grill or broiler. Spray grill rack with cooking spray.
Remove the steak and vegetables from bag and discard marinade. Place the steak and the vegetables on grill rack and cook 4-7 minutes on each side or until desired degree of doneness. Cut steak diagonally across the grain into thin slices. Cut peppers into thin strips. Cut onion slices in half.
Divide steak, bell peppers, and onion evenly among tortillas and top each with 1 tablespoon chipotle salsa and 1 1/2 teaspoons cilantro.