When speaking of "ancient times" we should really define more precisely who do we talk about - there were a huge differences between say citizens of Ancient Rome and some tribesman culture of Amazonia in terms of exposure to the pathogens.
We nowadays live in more sterile conditions, but we also live in a way bigger communities than ever, with significantly more population mobility - which makes us on average potentially exposed to a much wider spectrum of different germs in one's lifetime than it was a case ever before. When modern ppl get in contact with isolated tribes, although they're living whole lives in totally non-sterile conditions, it's almost always the modern people who will make them sick, not the other way around.
We nowadays live in more sterile conditions, but we also live in a way bigger communities than ever, with significantly more population mobility - which makes us on average potentially exposed to a much wider spectrum of different germs in one's lifetime than it was a case ever before. When modern ppl get in contact with isolated tribes, although they're living whole lives in totally non-sterile conditions, it's almost always the modern people who will make them sick, not the other way around.