What I understand is that some cultures, that have traditionally eaten dairy, haven't had large rates of diary intolerance until recently. There are cultures where drinking milk has been happening for thousands of years. The theory is that homogenisation and pasteurisation of milk, as well as modern industrial diary farming practices have changed milk fundamentally, and so humans find it difficult to digest. I say theory because there hasn't been much science done on this, but there is alot of empirical evidence from people who have tried these things out for themselves. Homogenising milk changes protein structure, and pasteurisation kills beneficial microbes necessary for digestion. We can no longer talk about milk as one thing. The milk I drink (raw, organic, cow) is a different food than what most people buy at the supermarket.
Also, many other modern practices affect digestion, from our general diets, to lack of exercise, stress, environmental pollutants etc.