There's a few key things you need to have to properly apologize[1]:
- a detailed account of the situation
- acknowledgement of the hurt or damage done
- taking responsibility for the situation
- recognition of your role in the event
- a statement of regret
- asking for forgiveness
- a promise that it won't happen again
- a form of restitution whenever possible
Most of those things aren't there. And, most notably, Jeff spent the majority of this post explaining why he wasn't at fault. That may be a fair opinion, but keep your ego to yourself - don't post an apology if you don't mean it, and don't act like this fulfills Gruber's request just because you put it on the internet.
Furthermore, Gruber is right. He has a license on the name Markdown[2] - the name is not up for grabs. And the name "Standard Markdown" very directly implies that the rest of the "flavors" of Markdown are wrong. I would say "Common Markdown" is no better - it implies that all other flavors of Markdown are uncommon. If Jeff really had any intention of making things right, the least he could have done was wait more than a day to hear back from Gruber - it's not like this is really a time-sensitive matter.