Airports are rarely next to your starting or ending locations, so flying usually requires extra ground transport on either end. This transportation, and the transfer time easily add an hour. Train stations are often close to the city centre, and better integrated into the local transportation networks.
In the airport, there is processing time before boarding - check-in, security, gate check, etc. This time adds another 45 minute buffer before departure. Boarding a train can be as simple as arriving at the terminal and walking onto the train.