Nothing is going to filter air-borne viruses effectively but it's unlikely that they are going to infect you after passing out of a host, through the air, through the on-board circulation system, back through the air and through your defenses (both structural and humoral) to get you sick.

Dander and other allergens are a bigger risk with unfiltered air. Now that everyone seems to be flying with animals (amazing how many Chihuahuas they are training now as "guide" animals), it's an issue. Ask your flight crew about cabin filtration maintenance and make sure it's been done at least as currently as the cockpit/crew filtration. Ask beforehand to see a log if you're really concerned.