it seems that it should be possible to create a mechanism which could cover these fees for open-source projects. Perhaps someone like Mozilla or Canonical or other open-source advocates could create a fund for such things?

Since the fees are capped, some organization could just pay the cap, distribute a "free" codec, and write the cost off as a marketing expense. Mozilla can afford to do this, but refuses on principle.

Is there anything like this for .mp3 support?

Fluendo distributes a "free" MP3 decoder; they pay the license fee on behalf of users.