I think the reason why the characters have Gas Mask is not necessarily because they will be affected but maybe because there are large pods of plants that will explode and suffocate Joel and other survivors where the infected people will be much stronger around those certain points.
From Game Informer info.
"The fungus needs a high dose of spores in a small area to infect a person. In dangerous areas gas masks can counter the threat. Those that test positive at military checkpoints are executed instantly."
There. That's why gas masks are in the game for this reason. I'm sure there will be areas where you have to wear it.
Bill wears a gas mask. If you look at the video again you will notice that Joel doesn't have a gas mask.
Maybe this is why Bill reacted so harshly by handcuffing Ellie and pointing his gun at Joel - perhaps the close proximity with the infected and Joel and Ellie not wearing as masks sparked his defense. Just an idea
The Planet Earth documentary said that the Cordyceps grows out of the insect and then release's spores into the air infecting the rest of the colony and if ND is staying true to the real parasite than I think the virus will be air born.
If they're going to play it like that, as in, the air around the infected is contaminated by cordyceps spores, then Joel and Ellie came dangerously close in the VGA trailer!