Melt the butter in a large skillet over medium heat and sauté the sliced red onion until translucent, about 2-3 minutes.
Add the tomatoes, bell peppers, salt, pepper, oregano, red chili flakes, and ¼ cup water. Reduce the heat to medium-low, and simmer, covered, until the tomatoes are soft, about 5 minutes.
Crack the eggs over the veggies, sprinkle a little more salt over the eggs, cover, and cook until the eggs are cooked to your liking.
Serve with Mexican crema (or sour cream), chimichurri, Cotija cheese, and fresh cilantro on top.