In a post apocalyptic setting, when a virus wiped out the vast majority of our population, society is based on small settlements, barely surviving. The world is changed, nature is taking over. Lets say that 98-99% of the population is gone, and a setting is happening two generations after the "worlds end".
Taken in consideration that "old world" technology is preserved, even though the knowledge to create again is lost due to population disappearance, in my opinion, there is nothing more frightening then a group of humans anywhere with proper tools. Would like that to not be the case.
I have a problem of coming up with a type of creatures, a species, or something similar that will keep humans "in check", and in some manner make travelling, inter-settlement interactions, hunting for food, spreading across the vast land for farming etc. much more difficult. Basically a thing that is kind of preventing people from advancing from their current state of life, that they have to confine themselves in protected settlements, to keep the outside world out.
I had some thoughts of maybe evolving currently existing predators (wolves, bears, bobcats, coyotes and so on) to be bigger, meaner, smarter, but I don't think that is enough to "keep us in check". Nor it is ecologically sustainable. If a number of carnivorous predators raise, in a matter of years the number of the hunted grazing animals will fail dramatically. If rats were to evolve in the ruins of the cities - what would sustain them, what would they eat after humans have are gone and the nutrients that come with them too? Maybe introduce a whole new species?