From the release notes:
In Flash Player 10.1, H.264 hardware acceleration is not supported under Linux and Mac OS. Linux currently lacks a developed standard API that supports H.264 hardware video decoding, and Mac OS X does not expose access to the required APIs. We will continue to evaluate adding the feature to Linux and Mac OS in future releases.
So, is there any realistic hope of H.264 acceleration ever showing up under Linux? This sounds like a more polite way of saying "we don't care."