The fuel in your tank helps to cool the electric fuel pump, which frequently generates a fair amount of heat as it runs. Thus, chronically running the car with a very low level of fuel in the tank does expose the pump to more heat than if it was run with a higher level of gas in the tank. Heat does take its toll on most things, including electric motors.
All of this leads me to the inevitable question:
Why not just fill the tank sooner, rather than always waiting until the last possible moment? If you made it a practice to fill the tank every time that it fell to the 1/4 mark, you would not spend any more time in gas stations than if you consciously decide to wait until it is almost empty.