What will keep beans tough, though, is acid, so never cook beans in wine, and limit tomatoes as well. I love beans and tomatoes, but I only unite them after the beans are fully tender.
The “liquor” left over from cooking beans is fantastic, full of flavor and body. Use it as a base for soups or for moistening pasta, and when you’re reheating a simple bowl of beans, always include some of their cooking liquid. I let the cooked beans cool in their liquid and I store them with their liquid in the refrigerator.