You could say the same of all Web technologies. Do you actually think it would be better to have software patents and royalties on every Web standard?

For one thing, this would be catastrophic for open source projects (and indeed commercial audio and video codecs have been a huge pain for open source developers and users). Well, you're suggesting that free codecs are bad because they profit Facebook, and you could say the same about open source software, especially those that get contributions from Facebook.

I rather think that advertisers will always pay money to advertise, and when some of that money goes to developing open and free technologies that's a good thing.

There are many free lunches. You can get a universally supported free video codec to use for your hobby project or for your company's product, without having a Facebook account. It is always possible to find hidden costs in free products, so what? You can do the same for paid-for products. The idea that a Blu-Ray player won't spy on you because the manufacturer paid some royalties is... flawed.