Software vs Hardware control
It usually means when used as a GPIO software can control whether it is an input, output, enabled and so on.  Basically software defines how the pin works.  In a micro controller there are often hardware functions, perhaps multiple select-able hardware functions such as I2C that also come out pins.  In this case you would do whatever needs to be done to put the pin under hardware control.  So it becomes no longer a GP pin but an input or output pin of an internal hardware block.