While what you're saying is true, the royalties side of things has been locked down by Google's legal team very effectively. If said patent holder makes a patent claim against WebM they automatically destroy all free royalty rights for themselves on the same codec (if I understand correctly). This means that while they could try to hold Google (or any other user of the codec) to some kind of patent royalties, Google could retaliate for any use that company or individual makes of the same codec (with as much leeway to set a price as the patent gives the original individual or company.

This is the true genious of the WebM license. It means even if this does happen in the future, Google can destroy whoever has this patent through a massive counter. It also means that any challenge would have to be made extremely carefully.

edited for spelling :)