During the infection the Pegasi took up as arial snipers, shooting the infected down from above. In doing so the Pegasi became superstitious that if they touched the ground, they would become infected since the infection is plant/fungal based, they would only land in Cloudsdale. Only later do they learn that with the spores emitting from stage 4 corpses they can still become infected.
Rainbow Dash however would still touch the ground to save her friends in a pinch.