stimmer:
Running your code, I only get 10.67KHz (~330Kbyte/sec) (I cross checked with stty -F /dev/ttyACM0 raw ; time cat /dev/ttyACM0 >out )
Wow, that's quite a difference. I am running on a very fast desktop machine (an i7-3930k) and I'm using the Due beta hardware, since the release Dues I purchased on still on backorder. Still, I wouldn't expect such a huge difference.
Edit: I noticed you're redirecting the data to "out". Sending to /dev/null might be a better test? On most modern PCs, I wouldn't expect this to make much difference. But in the early days of testing Teensy 2.0, I saw a laptop where attempting disk I/O in the same test as USB caused a significant slowdown. The same test on a desktop machine (both a few years ago) showed nearly the same speed with and without disk I/O.
If you post a complete benchmark program and specific steps, I'll run it here and share the results.