Can you have a quick look at the output of dmesg? When I connect my Due it claims to be a high-speed device! If that's true then I guess we're not being limited by the maximum theoretical speed 
I tried to do a loopback test - I didn't save the code but it would probably have just been something like:
if(SerialUSB.available()){byte c=SerialUSB.read();SerialUSB.write(c);}
I only got about 230Kbyte/sec into the Due - but most of the data was lost, only short sections near the beginning and end got copied back. Something to look into.
Running your code, I only get 10.67KHz (~330Kbyte/sec) (I cross checked with stty -F /dev/ttyACM0 raw ; time cat /dev/ttyACM0 >out )