I have a few thoughts on this. My main idea is that in the past, many people were farmers. I know my ancestors on my mother's side at least were, and that's the side I suspect those crazy genes came from that makes me such a square peg in a society of round holes. The farmer had his routines, and he often worked in solitude. He didn't have to multitask in a brightly lit, people-filled, noisy environment that was constantly changing. In the rural setting, he worked year after year in a predictable cycle (okay, there were droughts and such, but everyone was worried then). His neighbors knew him from babyhood, and the extended family was near by. He encountered very few 'new' people. If he was an Aspie, people just thought of him as a quiet, reserved person, or maybe somewhat eccentric. Life was slow. The fastest thing that happened was going to town on Saturday night and church on Sunday, and he probably knew everyone he saw very well. So, he didn't stand out--his daily environment didn't 'out' him.
Another idea I had is that something has changed in the physical environment that has altered our genes. Could it be the kind of prenatal care our mothers had? I know my mother was the victim of medical idiocy that dictated a pregnant mother should not gain ANY weight (even when the mother was not anywhere near overweight to begin with). She often told me horror stories of how her pregnancy with me was a time of starvation. I think she found a better doctor when she was having my sister, who is 100% neuro-typical. Then our mothers were told nursing her baby was 'dirty' and something only 'poor' women did. Wouldn't that mess with a baby's neurology?
Or perhaps we've just come up with labels to describe every possible variation on human personality. Maybe once upon a time, differences weren't so important, and more tolerated. Today, the pace of life is so fast, and things change quickly. Kids spend more time in social settings with age peers, supervised by people other than their parents.