Every time I fly, whether a long international flight or a short flight in the states I ALWAYS get the dreaded sinus infection. Here's what I'm going to try b/c I think it is both a dust/germs issue and a pressure issue:
1. Rinse your sinuses with ocean nasal rinse and get everything out before the flight.
2. Buy and wear a surgical mask (it may look dorky, but I'm sure it will be worth it).
Both the Ocean and the mask can be bought at CVS or any pharmacy. Good luck. I'll let you know if it works for me!