Come at it from the story.
You got me thinking about this. What inherited thing could protect from flu? Maybe IL-4 deficient persons would have less severe flu? Those people might be more susceptible to parasitic infection, and asthma, and maybe have poorer memory, and maybe be more sensitive to pain. But how to make that into an interesting story? The fact that your characters struggle with hookworms is hard for me to hook to the engine of a narrative.
A lot of heterozygote advantaged persons have no particular phenotype - for example sickle cell trait. Not a lot different about those people. It is not until they get together and have a homozygote baby that you see the phenotype manifested more - sick babies. I guess sick babies give a story some energy.
So the story: I picture your story like Stephen King's The Stand: everyone dying of flu except his few characters, who do not get sick. In your story, the people who do not die might know how they are different or maybe not. Maybe they are all descended from Latvian immigrants. Maybe they are a bunch of random folks who share in common a propensity for asthma or sensitivity to pain or poor memory. But really they can be whatever you want - after the flu apocalypse the survivors are unlikely to be doing molecular biology to elucidate the basis for their resistance.
Some phenotypes will be more helpful for your story than others. Flu is so complicated that if you assert these folks are resistant and are different in other ways (that you choose) and leave it at that, that will be good enough. If, for example, you assert they are deficient in IL-4 and try hard to get into those weeds I think (having just done that!) it will be a distraction from your effort to write a compelling story.
It occurs to me that instead of molecular biology, the basis for resistance could be something very different. Not a receptor or a cytokine but something more than that. Maybe something fundamental about the interface between human and world. And when the first homozygote baby is born it is not sick; not at all. But it is even more different than the parents. It is the next step in human evolution after the flu bottleneck.