Bean are less than 2% fat, they do have some protein.
For hundreds of thousands of years, humans were hunter-gathers, their diets consisted of meat, fruits and wild greens. even after the rise of farming most groups still relied mostly on hunting, with farming being for food-supplementation or for times when hunting was not possible.
Even those cultures that have survived off of these things have only been doing so for the last 8,000 years or so.
The idea that "bread, rice, and beans" are the historical human diet is a vast modern oversimplification, for 95% of history, people ate meat, fish, eggs, veggies, fruits, nuts, and potatoes. this diet you're talking about has only very recently risen and it has lead to a massive explosion in population, sure, these foods will keep you alive and even allow you to have kids and even keep those kids alive, but being alive is not being healthy. It's not complicated.
Why do you think third world counties that live mostly off of bread rice and beans are so fucking retarded and unhealthy? Africa? India? They aren't healthy, they're stupid and ravaged by illness.
It amazes me how little people understand about nutrition, and how upset they get when presented with the basic fact that you need to fucking eat meat and vegetables.