Their breeding strategy required massive colonies to fill the local predators' bellies and still have survivors. They didn't really count on a predator that would take entire colonies. Nets, alcohol soaked grain, fire arms, explosives, coupled with a huge national demand coupled with a vast transportation network were nothing like foxes, snakes, and birds of prey.
Musk oxen have the same problem. "Back into a mass protecting the young with your heads facing outward" doesn't work well against rifles. They don't have much of a plan B. Being dark on a barren, white landscape much of the year also sucks.
Many of the pelagic fish also fall into this category. They aren't built for a predator that will scoop up an entire 4000kg school of fish in one swipe.
From that perspective, it's not very surprising that human-targeted parasites haven't been going extinct without substantial purposeful effort, because their host has been very successful at increasing and spreading its population. If you think of the human population as the relevant "environment" for those species, then the environment is in very good shape...
And humans, with their ability to thrive in basically any climactic zone, are the ultimate pest species. No wonder that vectors that spread human disease are also so successful -- so much meat to prey upon.