Heat oven to 400°F. Spray 9-inch glass pie plate with cooking spray. In medium bowl, mix chiles, beans, onions, tomato, 1/2 cup of the enchilada sauce, the pepper Jack cheese, 1/4 cup of the cilantro and 1/2 cup of the Cheddar cheese; set aside.
Spoon 1/4 cup enchilada sauce into pie plate. Top with 1 tortilla and 1/3 of the bean mixture. Repeat twice to make 3 layers. Top with remaining tortilla. Cover loosely with foil.
Bake 30 minutes. Uncover; sprinkle with remaining Cheddar cheese. Bake 5 to 7 minutes longer or until cheese is melted. Sprinkle with remaining 1/4 cup cilantro. Serve with salsa if desired.