Preheat oven to 400. In a medium saucepan, heat oil over medium-high. Add onion and cook until translucent, about 8 minutes. Season with salt and pepper; add garlic and cook until fragrant, 30 to 45 seconds. Add flour and stir to coat. Pour in tomatoes, scraping up browned bits. Add red-pepper flakes and season with salt and pepper. Cook until tomato sauce is thickened and bubbling, 2 to 3 minutes. Stir in half-and-half and remove pan from heat.
Spread 1 cup tomato sauce in a 9-by-13-inch baking dish. Place tortilla strips in an even layer over sauce. Spread remaining sauce over tortillas. Break eggs over top and sprinkle with cheese. Bake until sauce is bubbling and egg whites are set, about 25 minutes.