I agree with you here, but it is easy to screw it up. Early Arduino UNO models had to have the USB bridge's firmware updated because someone forgot a compiler flag, which resulted in a difficult to troubleshoot bug that would effectively 'brick'[1] some boards. http://arduino.cc/en/Hacking/DFUProgramming8U2

[1] Not really bricked, but bricked to someone who is expecting an Arduino, and new to microcontrollers.