ZDoom

Would any of the complaints in this have been relevant on why ogg has not been used, by chance?

http://hardwarebug.org/2010/03/03/ogg-objections/

As someone who's only at a basic level of programming, I can only understand a few things here, but it seems plausible and I figured I'd get some more informed opinions.

Well like any criticism of Ogg, Theora, and Vorbis you can find just as many arguments telling you the opposite. But lets assume for a moment that everything on that page is valid. Ogg isn't the only free container format, there is also Matroska which is used for the WebM standard (Matroska with VP8 and Vorbis) set by Google. If the container was the issue at hand an alternative would have been found, so the decision is basically just on the codecs themselves. I should mention that the video codec is the only thing I've seen a heated argument on. I don't think there were any objections to Vorbis which is probably why Google is using it for WebM.

I find it sad that HTML5 was doomed from the start for having the misguided notion that several rival companies could agree on a standard.

Of course, AFAIK it isn't finalized yet, so who knows what may happen. If they actually do agree I'll be surprised.