Pretty much all schedules are padded, such is the unpredictable nature of flying. And, in busy airspace, surely a pilot has relatively little say in the speed that they fly at? On longer flights there's more variation, but still.

There is, however, plenty an airline can (and does) do to make up delays. They can request more direct routings, make efforts to speed up boarding and cargo/luggage loading procedures, try to make sure they don't get put to the back of the queue for departure or arrivals (and for a gate at the destination airport, should it be a particularly busy one).

Just because they're speeding things up doesn't mean the plane's actually moving more quickly once it's up and away.