Air is denser the lower you are in the atmosphere so a plane's cruise speed is actually a lot lower at 1000 feet than at 30,000 feet.

So the optimal altitude to climb to and fly at most of the flight for shortest possible flight time depends on distance (since it's a balance between climb time, descent time and speed at the cruise altitude) as well as on the direction of the wind at the cruise altitude since a tail wind will actually help getting there faster (so a choice of a lower cruise altitude might yield a better time because the wind is in the right direction there even though the air is a bit denser lower down).

This is of course all theoretical since commercial planes don't get much choice in terms of the cruise altitude for their flight.