H.264 seems to be the most widely supported format today, if you don't get screwed by the whole patent mess. A significant class of users do, though, if only because they use OSS browsers that are never likely to support a royalty-encumbered format. And of course, if you're distributing H.264 videos you probably need a lawyer one way or another.
As for customisation, Flash offers all kinds of possibilities that HTML5 video just doesn't, from custom controls to copy protection. Some people might not care, but they're probably the same ones who object to table-based layout and then expect you to write 20 lines of CSS and import three different IE-specific stylesheets just to get a trivial layout. Check out past comments from people who work at places like Google/YouTube.
ah, that brings back good old memories. We used to prepare at least three formats for WMP, Realplayer and Quicktime. AFAIK HTML5 isn't doing anything better.
Hypothetically were IE to ship with WebM support, Apple doesn't have the market share to enforce their current codec monoculture. The converse is not true however; Microsoft doesn't care if Safari/iOS can play WebM. The onus is thus on the IE team, and I think Apple is irrelevant to the issue.