Mayan were more isolated, I suppose.
Well, to start with, they had a substantial population density. Knock back 50% of the population to epidemics, and they could breed back within a generation.
Secondly, they were an organized agricultural society. That meant that most of the time they had ready access to stores of food and water. That's important.
Hunter/Gatherer societies were disproportionately devastated because their lifestyle meant much higher mortality rates. If you're going on a hunter-gathering lifestyle, there's no accessible surplus available. You're basically hunting/gathering your dinner every day or every few days. That's fine when you and yours are all healthy and hale. But if you are really sick and incapacitated, then you add starvation and dehydration on top of things. You die, where you might have pulled through if you'd had more access to food and water.
It's not a complete answer. But it's a start.