Bring a large pot of salted water to a boil. Stir in the pasta and cook it according to the package directions, until al dente. Drain the pasta into a colander when done.
While the pasta cooks, coat the bottom of a large pot with 2 tablespoons of oil and place it over medium heat. When the oil is hot, add the onion and pepper. Cook them, stirring frequently, until the onion is soft and translucent and the pepper is tender, about 5 minutes.
Add the garlic and sprinkle in the flour. Cook the mixture, stirring constantly, for about 2 minutes.
Stir in the coconut milk, tomatoes, black beans, kidney beans, nutritional yeast, chili powder, cumin, and hot sauce. Raise the heat and bring the liquid to a low boil. Lower the heat and allow the mixture to simmer for about 10 minutes, until the sauce is thick and creamy.
Stir in the pasta, and continue cooking the mixture for a minute or two, just to heat the pasta back up and meld it with the sauce.
Remove the pot from heat. Season the mixture with salt to taste, and adjust any other seasonings to your liking.
Divide into bowls and top with fresh chives, if desired, and serve.