Given that the 'bugs in aircon' thing is an urban legend, maybe someone can explain why many people seem to have a cough or cold after a flight than at any other time.
I am quite sure that all decent airlines do their best to ensure that the air is clean and adequately filtered, in the interest of their own staff and the passengers, so I am not disputing that, but there does seem to be a factor that causes coughs and colds.