In short - viruses can actually harm your immune system and lead to long term problems. OTOH, we co-evolved with certain parasites that can help us.

Airborne pathogens are not likely to be the helpful type we’ve co-evolved with — they’re much more likely to be the type we’ve only had to deal with since the creation of higher density living and rapid long distance travel. Therefore air filters are likely to help children’s health both short and long term.