I don't buy the "we're a poor non-profit" bit that people keep attributing to Mozilla - did they ever say that? Their income in 2009 alone was over $100m, pretty much all from google. I can believe it's an ideological stance though.
It's not quite that they can't afford to pay per-end-user licence fees, it's that the Mozilla open-source licence, like all good open-source licences, explicitly and by design precludes them even
knowing how many end users they have, or even how many sublicensees (forks). Under those circumstances there's no way for them to honestly sign any licence agreement that the H.264 patent-holders would tolerate. So in that sense yes, it's an ideological stand.
I'm pretty sure that they'd just be able to pay the maxed-out fee (where it gets capped) and call it a day... I'm also sure that every big H264 license has been negotiated in one way or another, even if it is just to keep the lawyers off the streets.
As for HW accelerated WebM decode - recent video decode engines tend to be more programmable than the older ones which were very very hard coded in silicon for maximum efficiency... but there could well be many roadblocks that prevent any current hardware from being able to effectively hardware-accelerate WebM decode (it doesn't take much to throw a spanner into the works of hardware that's been highly optimized for existing standards).
But Protocom were insane even in their heyday. I'm sure programmable hardware is the norm these days, if only to avoid having separate hardware for MPEG2, H.264 and VC-1. In my distinctly inexpert opinion, you'd be unlucky to design hardware that could accelerate all of those but not WebM.
You'd be surprised, then; it's not a case of accelerating (eg some DCT work), the hardware tends to do the entire job - point it at a bitstream and a framebuffer and off it goes. Some are programmable (ie you'd load an H264 decoder into it then set it off... though they're not general purpose CPUs) but many are not.
They're hardcoded often because the companies in question had the IP lying about, all nicely optimized and low power from previous generations of parts used in things like DVD or Blu-Ray players.