I should also point out that media containers were not originally designed for random things being distributed over the internet. Rather, they are for developers to author and users to play back.
As a professional, if I put stuff on a DVD or a Web site that the average computer user couldn't see, that disc or site would include whatever drivers or CODECs one needed in order to video my media. That's still pretty much the rule.
This is very useful for professional work. For example, I bought a license for the Cineform CODEC, which is an "intermediate" CODEC, designed for fast editing of computationally expensive formats like MPEG-2 and AVC. Not so expensive on their own, but try doing 10 or 20 layers of video in a single project, and you'll meet "slow" on any PC. The multimedia frameworks allow video and audio editors to use new CODECs without any changes to their own code.
At the fringes, sure, you have pirates and crazy people putting weird stuff inside AVIs, without telling you what it is. But this is not a general problem.