Since the air pressure on a plane differs from that on the ground, fresh air must be continuously pumped into the cabin. Although the air is clean, it's very dry and can leave you with a scratchy throat if you don't drink enough. Doctors themselves even recommend staying hydrated while on a flight to help your body both adjust and recover from the long and stressful journey of air travel.
Lots of people end up catching a cold after a flight, and that's because of the general air quality. Water is a great preventative measure; hydration can stop a sore throat.