Then Tony would work/drink himself to death, probably wisecracking the whole time.
But imagine that Tony, who's definitely all about the security measures, can hermetically seal and sterilize a building the size of a skyscraper and then ventilate it only through super duper filters, plus he can fabricate pretty much anything in his awesome workshop if he has raw materials and power. Imagine the non-immune people who live their lives in that building as they try to find a cure or a vaccine.
Or, the Marvel Universe being what it is, a counterspell.
ETA: OK. *cracks knuckles* Here we go.
CAPTAIN AMERICA is immune: He fights the good fight on the front line against trolls and beasts (zombies and monsters, they would probably call them), protecting a little colony of survivors in the ruins of New York City, probably in an area where the subways and so forth would have flooded within days of total social breakdown to prevent (as many) attacks from below. (If the pumps ever stopped, parts of NYC would have about two feet of airspace in the subway tunnels within days.)
IRON MAN is immune: Pretty much as above, except with a hermetically sealed building and a kickin' science lab. And JARVIS.
HULK is immune: Banner welcomes the rage because he doesn't have to see the horrors around him. As Hulk has more and more time on the outside, so to speak, he gains increasing control over himself. Nevertheless, Banner keeps waking up in unfamiliar places and has resigned himself to this. They live alone, because the other survivors are afraid of them, but they keep the big baddies away from the survivors' homes wherever they happen to be.
FALCON is immune: He stays aloft with the birds for as long as his wings hold out, protecting a colony at the top of a skyscraper while scouting ways out of the city, hopefully to an island they can burn off and recolonize.
SPIDER-MAN is immune: About the same, but with a young scared kid in the costume. Also people tend to freak out when they see him shoot webbing, because goo monsters.
BLACK WIDOW is immune: A deadly shot, she stockpiles firearms and charms her way into the survivor colony with the most level-headed types unless they're total scumbags, in which case she shoots them and takes over. She trains a generation of fierce little girls to protect their families. One shot, one kill.
WINTER SOLDIER is immune: About the same, but with more blackouts.
HAWKEYE is immune: The same again, but he raises an entire village of archers whose deadly hand-made longbows hold their land safe.