Cook the beans: Heat oil in a saucepan over medium heat. Add onion, bell pepper, and red pepper flakes. Cook, stirring, until pepper is tender, about 8 minutes. Add beans and liquid and bring mixture to a boil. Reduce to a simmer. Cook, stirring, until slightly thickened, about 5 minutes. Season with salt.
Prepare salsa: Combine tomatoes and onion; season with salt and top with crumbled cheese.
To serve: Heat tortillas in a dry pan until warm. Spoon rice and beans over half. Top with avocado. Fold into quarters. Serve with lime and salsa.