Actually I find my digestion improves on a bean/veggie/brown rice diet, vs. a typical diet of meat/refined starch/etc.
The "flatulence factor" (scientific term) in beans is primarily due to a type of carbohydrate called an oligosaccharide: oligo for "few", and saccharide for "sugar". These sugars are linked together in the oligosaccharide by bonds that humans lack the enzyme to break. So they are indigestible by humans. When the oligosaccharides hit the lower gut, there are plenty of bacteria able to break the bonds and the result may be excess gas.
Soaking the beans helps to leach out the oligosaccharides. But it's also been shown that soaking overnight can enable a harmless bacteria to attack the bonds in the beans themselves. In other words, it's a type of fermentation. Other fermented bean products, like tofu from soybeans, are not flatulence causing becaus of the frementation process. Of course one must discard the soak water and cook in fresh water, and of course cooking until the beans are tender is required for optimal digestibility. The trick - which native americans have practiced for centuries - is to save a little of the soak water to introduce into the next batch of beans, increasing the chance that the oligosaccharides will be even further reduced.
Don't know if the bean protein is particularly indigestible. Do know that soy flour - from which the protein has been removed - can have high levels of the oligosaccharides that cause flatulence. And a lot of our processed foods contain soy flour these days.
