In a medium saucepan heat olive oil over medium heat. When hot add onion and cook, stirring occasionally, for 3-4 minutes until starting to soften. Add garlic cook for about 1 minute until fragrant.
Mix rice, tomato, chipotle peppers, adobo sauce, and salt into the saucepan. Stir in ¾ cup water and bring to a boil over high heat. Cover, reduce heat to low, and simmer for 15 minutes. Remove from heat and leave covered.
While rice is cooking, preheat oven to 400º. Cut peppers in half lengthwise and remove stem, seeds, and membranes. Grease a casserole dish or 9x13-inch pan with oil or nonstick spray. Place peppers in pan and set aside.
When rice is done cooking uncover and mix in beans, black olives, and cotija cheese.
Fill peppers with rice mixture. Top peppers with shredded cheddar cheese.
Add 1/4 cup of water to the bottom of the baking dish. Cover with foil and bake for 30 minutes or until peppers are tender. Remove foil and bake for an additional 5-10 minutes until cheese is completely melted.
Serve peppers topped with cilantro.