Burnt USB chip, HELP!

Does anyone know of a way to communicate with a mega board if the USB chip is fried, but everything else is OK. ?

try this http://arduino.cc/en/Main/Standalone, mixed with http://arduino.cc/en/Main/ArduinoBoardMega, you have "only"to solder you new FTDI board pin tx, Rx, reset, Vcc and GND on the right pin of broken FTDI chip ;D
take a look at the schematics, seems more complicated but X3 are used to burn the bootloader and nothig else, then we need GND, +5V,(the “strange” link are done on the FTDI board so don’t care) TX and RX. Seems thaht GPIO1 and GPIO2 turn on some led to show you when TX/RX is working… well i hope it will not be a great loose. You need only a new FTDI board