LHR is closer to both MAN and London Euston, so why fly?
Whilst the train and APD have impacted MAN-LHR numbers, the route still carries large numbers of connecting passengers which BA and VS need to feed their LHR hub. Many of these passengers would tend to go via competing Euro hubs if the BA and Little Red MAN-LHR flights didn't exist, rather than haul their luggage on the train to London Euston and then out again to LHR just to then connect to other overseas destinations.
Many of the sun and low cost routes out of LGW are now also available from MAN (and other regional centres), so the reason for BA and Virgin to provide a MAN-LGW feeder service as well as LHR is not as apparent. And as DJ says the train is now a frequent, cheaper and more convenient option for much of the MAN-LON point to point market.