From the perspective of an airline, is it just to avoid penalty and also to portray reliable service to the customers? Or is it just a matter of logistics and scheduling?
I can think of a few:
Any delay in the flight is a waste of valuable resources- the flight, cabin and ground crew who have to be paid and the aircraft itself, which is not generating any revenue but costing money for the airline. Also, the airline may have to pay for the time the aircraft spends in the airport.
There is an economic cost associated with on-time performance- for example, passengers are more likely to take airlines which have better on-time performance over others.
Another case is that of customers taking connecting flights- again, on-time performance could be the difference here. This means loss of business for the lower performing airline.
For airlines operating multiple trips per day, the delay and the associated costs are cumulative; for example, if the first flight of the day is delayed, it snowballs into the day- requires replanning for the rest of the day in other airports and causes further delays.
For the airline industry, the delays cost billions of dollars every year (1 and 2) and can reduce the operating revenues by a few percentage points (3). The table below, taken from the NEXTOR report on Total Delay Impact Study shows the cost to US airlines due to delays.
As can be seen, the the costs due to delay to airlines are quite high.