The Arduino IDE only allows a programmer to be used for boards of the same architecture as the hardware package that defines the programmer. The Arduino as ISP programmer definition is part of Arduino AVR Boards and as such can only be used for boards of the AVR architecture. The Due's architecture is SAM. Unfortunately the Due's hardware package does not define any programmers, which is why you encountered that error. So the official software does not provide any way to do a Tools > Burn Bootloader operation on the Due. If you do some searching you might find a workaround for this.