The fuel pump neither knows nor cares if the tank is full or nearly empty - all it needs is to have some fuel. The tank and pickups are designed to ensure that the pump is wet all the time, only causing a possible problem if you actually run out of fuel. If you always fill up at 1/4 or 1/2 a tank not only are you filling more frequently (your choice) but also constantly carrying 5, 6, 7 gallons of fuel around with you that you are never going to use. I get the emergency cover thing, and when there's a run on fuel this seems prudent, but under normal conditions I see no reason not to use all the fuel you have paid for and carried around with you - or as much as is possible. I'll happily run to the fuel light on all my vehicles, knowing that even when the gauge says 'E' and the range says 0 there's contingency fuel left. I once drove around 30 miles after the range went first to "0" and then to "-" and still no signs of fuel starvation.
There is one train of thought that says that running low means you may pick up more of the sediment and water that can sit at the bottom, but also that frequently running to empty reduces the chances of building up a sediment or water.