Preheat oven to 350º Fahrenheit and lightly grease a 9×13-inch casserole dish.
In a medium bowl, mix together cream of chicken soup, diced tomatoes, onion, red peppers, sour cream, green chilies, red chili flakes, salt, and pepper until thoroughly combined, then spread a thin layer of sauce evenly in bottom of pan.
Add an even layer of taquitos to the pan, cover with remaining sauce, and bake for 25 minutes.
Remove from oven and cover with pepper jack cheese. Bake an additional 5-10 minutes or until cheese is melted and bubbly.