Arduino Due getting warm when powered on

Madbus:
even when no program is running on it.

Unless you are using sleep modes, microcontrollers basically run all the time. There is no "no program" running on it. The flash memory is continuously read, and the bit pattern will be decoded into an instruction. Usually when the flash memory is "empty" it’s all set to 1. In most microcontroller architectures this will be decoded as some simple instruction like ADD. So, the processor will just add something forever.

The same is in principle true for all digital computers, but the operating system is the continuously executed program when no user program is running. And modern operating systems are handling power modes, frequency scaling, sleep modes and so on.