Soybeans: Why We Don't Eat Them Like Other Beans

Even after lengthy boiling, soybeans remain quite tough and a little bitter. More importantly, due to a digestive enzyme called trypsin which interferes with protein digestion, soybeans are largely indigestible even after cooking. Most of the bean's highly valuable protein just passes through your system. No doubt it is for these reasons that the Chinese learned to process the bean in other ways before cooking and consuming. These processes include pressing oil from the beans, grinding and boiling to make soy milk, grinding, boiling and adding a coagulating agent to make tofu, and fermenting to create products like soy sauce and black beans. Whole fresh beans (ripe beans picked before they are dry and hard) are cooked in their pods and eaten as a vegetable.

Source: On Food and Cooking