Thrust device calls, like those of the underlying CUDA library, are asynchronous by default. The only exception is calls that result in a memcpy, which are synchronous. To wait until an async call is completed you need to call one of the synchronize commands, like cudaDeviceSynchronize.
Looking through his test.cu file, he snaps a timestamp using std::clock right after doing the kernel launch with for_each. Ignoring the fact that this is not an accurate way to benchmark a GPU (you need to use events to accurately benchmark the kernel) what you're capturing will just be the processor time it takes to make the async kernel launch. Std::clock measures CPU time, which is (rightly) close to 0 for a program that runs on the GPU.
It's entirely possible that you're not even getting valid results out of the other end - note that you don't show output. I don't know if thrust's magic device memory access function triggers a synchronization or not. I kinda remember having to make an explicit call when I did a GPU simulation.
I don't have access to a CUDA box at the moment, I'd have to add those cudaDeviceSynchronize calls after the for_each invocations to be sure.