Most a/c now use HEPA filters in the recirulating system. These are about 99.99% efficient in the removal of particulate contamination including viral types. These types of filter are also used in laboratories dealing with radioactiveand pharmacuetical products.
Therefore the recirculated air is almost free of particular and viral contaminants. Travelling on a plane is no more risky in this effect than being on a train or bus. If you catch flu, it will be the virusses first trip and is unlikely to be as a result of the air being recirculated. The engineer changing the filter however, has a far greater chance of catching something.
HEPA - Wikipedia, the free encyclopedia may explain more.