Arduino Mega timeout communication with programmer error
The bootloader on an arduino is just a piece of software written to enable you to update your sketches using the usb connection. Without the bootloader you can't upload sketches using just the arduino ide.

More information about the bootloader can be found here: http://arduino.cc/en/Guide/Environment?from=Tutorial.Bootloader
Look under the heading entitled uploading which explains the part the bootloader plays in uploading sketches.

When you use the "Burn Bootloader" button in the arduino ide it will attempt to write a new copy of the bootloader onto the attached Arduino board. To do this the board must be attached in a specific manner - that is - using the icsp/isp header rather than the usb cable.

Now to program the avr chip directly you have to use an external (hardware) programmer. Fortunately you don't have to buy one if you have a second arduino because the second arduino can be used as a programmer. Instructions for doing so can be found here: http://arduino.cc/en/Tutorial/ArduinoISP

Even more info about the bootloader: http://arduino.cc/en/Hacking/Bootloader?from=Main.Bootloader