Sure you programmed the bootloader right?
Are you sure you uploaded the bootloader correctly? If you upload any other program, does it work fine? Tx/Rx not mixed up?
Since the USB chip fried, is anything still shorting? I recommend unsoldering the 3 pin diode next to it just in case. Its a tiny black chip with 3 pins sticking out, and relatively easy to unsolder. The USB chip is very difficult to unsolder, so removing the diode will cut power to it.