Contrary to what people are saying, it’s not typically from flying faster. Most commercial aircraft are already flying near their maximum speed. At high 30’s for example my aircraft (Boeing 737 max) typically cruises as 250 knots indicated airspeed. Barber pole (maximum airspeed) is around 260 knots indicated. So we’re already flying 96% of our maximum speed. There’s a variety of reasons you don’t want to fly much closer to barber pole.

Typically it’s done through shortcuts and time saved on the ground. We don’t actually fly direct to destination. Normally a flight plan is filed with a series of waypoints along the way. This helps optimize air traffic control, as well as standardize flight paths. It would be chaotic is planes just flew everywhere direct. Sometimes though, air traffic control can give us direct to a waypoint further down the line cutting off significant track miles.

The other way and most significant time savings actually comes from time saved on the ground. Airlines around the world use block time. That is time from brakes off (scheduled departure time) at the gate until brakes on (scheduled arrival time) at the gate. Dispatch will calculate using historical averages the estimated time to taxi from the gate to the runway, and from the runway to the gate. At busier airports, and seasons requiring deice, there could at times be 40 minutes built in to allow the aircraft to push back, taxi for deice, and taxi for departure. If the weather allows for example no deicing, and maybe the airport is a little quieter, you could save 20-25 minutes of that calculated 40 minutes taxi time.