If Humans Have Been Drinking Milk For Ages, Why Does It Seem That Recently There Has Been A General Rise In Allergic Reactions To It?
It is lactose intolerance, (the lack of the ability to digest the sugar lactose found in dairy) that you are probably interested in here, not the allergy to the various protein fractions contained in milk, that’s another (and much more serious) matter entirely.
An average of roughly 65% of the world population falls under the classification of lactose intolerant,  varying between regions, from less than 10% in Northern Europe, to as high as 95% in parts of Asia and Africa. This intolerance looks to be the default gene setting in many populations, with the exception of relatively smaller percentage of dairy-dependent populations whose gene mutations seem to have selected in favour of the conservation of the mutation of a lactase persistent set of genes. Members of these lactase persistent populations maintain the ability to manufacture roughly 10 times the average amount of lactase (the main enzyme responsible for the digestion of lactose) than that which is produced by individuals in the lactose intolerant population. These fortunate individuals routinely and happily consume large amounts of milk and associated dairy products with no problem whatsoever.
It has often been suggested that modern processing methods like homogenization, pasteurization, etc. are directly responsible for the supposed rise in intolerance. This is nonsense. As, mentioned above, the causative factor is almost entirely the result of a default gene mode, i.e. a dominant genetic trait for the underproduction of the lactase enzyme. The basic issue here is of completely genetic origin, not some menacing technological frankensteination of an earlier, supposedly more innocent, beautiful and pristine food product.
Technology, food technology particularly, may have the sins of the fatherson its collective conscience and blood under its well manicured fingernails, history provides countless examples of its f**kups, but technology also tends to provide salvation in the form of the tools with which to clean up its messes… and no, this is not one of them.
The drinking of milk and consuming of associated dairy products dates from roughly 8000 BC.. This habit coincides with the advent of agriculture and the beginning of the domestication of farm animals. I think that it would be fair to say that the ability to digest dairy products could be considered a helpful survival adaptation. Individuals who do not carry this ability to digest lactose might not necessarily be in a advantageous position should other types of food sources become scarce or depleted.
Estimates for the total world population 10,000 years ago run around 5 millions. Currently, in 2019, the world population is 7.7 billion. That makes the current population 1540 times greater now than it was in 8000 BC.
If 65% of the current world pop. is lactose intolerant, that’s just over 5 billion currently labeled with this condition. A rather alarmingly large amount of people to have walking around with embarrassing digestive problems, unpleasantly biliousness, presumably making a significant contribution to global warming through their intense methane and H2S production, isn’t it?
Not quite as bad as burning the Amazonian Rain Forest to a cinder or lighting up Arabian Oil Fields, but still, giving all the poor methane producing farm creatures those Militant Vegetarian Extremest have been indicting and pointing their boney fingers at a reason to point back.
So, to wrap this up and answer your question, the reason that it seems that milk intolerance is on the rise is the same reason it appears that incidences of gluten and peanut intolerances are on the rise, arguably more access to the products that cause these conditions, along with easier claim to media streams that allow the affected individuals a louder voice, enabling them to express themselves effortlessly, making these issues more explicitly available to the general population.
The processing methods of Modern Food Technologies for these foodstuffs are not to blame for the rise in perceived cases of Lactose Intolerance in this instance. Other than perhaps making these items more universally available, cheaper and easier to access, bringing to light the 65% of the population who are genetically predisposed in this direction.