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The ATmega2560 on the Mega 2560 comes preprogrammed with a bootloader that allows you to upload new code to it without the use of an external hardware programmer. It communicates using the original STK500 protocol (reference, C header files).
Rather then requiring a physical press of the reset button before an upload, the Mega 2560 is designed in a way that allows it to be reset by software running on a connected computer. One of the hardware flow control lines (DTR) of the ATmega8U2 is connected to the reset line of the ATmega2560 via a 100 nanofarad capacitor. When this line is asserted (taken low), the reset line drops long enough to reset the chip. The Arduino Software (IDE) uses this capability to allow you to upload code by simply pressing the upload button in the Arduino environment. This means that the bootloader can have a shorter timeout, as the lowering of DTR can be well-coordinated with the start of the upload. 153554b96e