I understand where you're coming from. It does seem very far-fetched. Like Shinigami said, it's probably that the plot is set in stone and anything that happens during the actual playing of the game is discounted.
I think (correct me if I'm wrong) that only the C virus was airborne, apart from the spores created from the Las Plagas fossils, but those spores only infected with prolonged proximity to the fossils. Only Leon and Helena's scenario in RE6 dealt with the airborne virus, which was produced by Lepotitsa and Haos. I guess that they managed to outrun the fog released from the missile in China. This is speculation, but maybe eventually the fog and virus dissipates until the concentration of the virus in the air isn't infectious. Maybe the virus can only survive in certain conditions, so once it's released, after a while, it dies. Who knows?
That might explain why Leon and Helena weren't infected in Tall Oaks. The virus could have been released in the banquet hall or wherever, and dissipated or the virus died soon after. Capcom could probably find a way to explain it.
I guess that, according to the plot, any open wounds that weren't covered by the characters were never exposed to any bodily fluids that the zombies/mutants produced. The characters were never bitten, injected or infected any other way (apart from Leon, Jill and Sherry but they were cured). Like I said, it seems far-fetched. But I guess that's the appeal of games. They give you an escape from reality.