If it's only for the iPad, then yes, go for it.
The major problem with HTML5 video is that there is no agreement over which format to use. At the moment, some browsers support H.264, some support Ogg Theora, some support both, and of course, IE 8 and earlier (and older versions of other browsers) support neither. See Wikipedia for more details.
Edit in light of the question edit: Here's a quote from Steve Jobs' recently posted "Thoughts on Flash":
...almost all this video is also
available in a more modern format,
H.264, and viewable on iPhones, iPods
and iPads. YouTube, with an estimated
40% of the web’s video, shines in an
app bundled on all Apple mobile
devices, with the iPad offering
perhaps the best YouTube discovery and
viewing experience ever. Add to this
video from Vimeo, Netflix, Facebook,
ABC, CBS, CNN, MSNBC, Fox News, ESPN,
NPR, Time, The New York Times, The
Wall Street Journal, Sports
Illustrated, People, National
Geographic, and many, many others.
iPhone, iPod and iPad users aren’t
missing much video.
Given the list of video providers using HTML5 video (because that's how this H.264 video is delivered), I think you'll be fine.
Apple has a list of high profile sites that "iPad ready". Most of these sites use HTML5 video (at least when the iPad is detected). One other thing to keep in mind is that navigation can be different on a mutli-touch device compared with a mouse.