It seems that the Mega boards (and maybe some others) have problems with the firmware that controls the USB communication. One can easily test if this is the problem by pressing the reset button on the Arduino board, just after the "fopen" command is issued (for the ArduinoIO this is when the "...." appears). For some reason the Arduino is stalled after establishing communication, and holding the reset for few seconds and releasing it will allow it to go back to life and to communicate with matlab.
Also note that: 1) You should not download the "combined" firmware file but the arduino-usbserial one: https://github.com/arduino/Arduino/blob/master/hardware/arduino/firmwares/atmegaxxu2/arduino-usbserial/Arduino-usbserial-atmega16u2-Mega2560-Rev3.hex
2) For download as HEX file, you must right-click where it says "RAW" and choose save-as.
3) If you are using Windows, after resetting your Arduino Mega 2560 into DFU programming mode (with the shortcut, as described above), you will need to install the driver for the FLIP software. Tell Windows to install it from: ..\filp 3.2.2\usb directory