The fact that an air intake borders our brain is a massive security weakness in our "intelligent" design (the quotes are for sarcasm). It's like allowing HTTP calls from your webservers to be routed, in some circumstances, to your not-firewalled, not-SSL, not-password-protected database. Like building a massive bank vault with all sorts of protective layers, then adding a small unlocked door that opens on the street.
I just hate that the smallest sinus infection can affect my overall system by producing massive headaches, or that these mofo organisms can just trek up my nose and feast on my brain cells. Clearly the Earth atmosphere is just too welcoming; selection on this trait was never forced, and here we are.
The minute we start making cyborg augmentations to improve filtering of our air ducts, I'll be the first in line.