it means that interfacing the GPIO pins with most exisiting arduino shield circuits should be done through a level converter.
A lot of 'older' arduino shields expect / use 5 volt for their IO but the due uses 3.3V for their IO...
Using a level converter or using optically isolated IO are 2 approaches to interfacing the DUE to higher voltage circuits.
The simplest option is the bidirectional level shifter circuit developed by sparkfun.
Alternatively if you are designing your own 'shield' or interface you could use the linked level shifter circuit as a basis for your own design... It is a quite simple and ingenious circuit and just works as intended... the mosfets and resistors are cheap enough to buy in bulk for incorporating a level shifter into your own circuits