I'd say "annoyed" rather than "threatened," and I think it's in part the name, yes. I see a lot of "naming variants '$foo Markdown' is common, what's the beef" responses and I get that, but Standard has very different connotations from Multi- or Github-Flavored or other past versions. I'm not sure that simply naming it something else would have solved this issue, but I don't think it would have hurt to pick something more like "Formal Markdown" -- which captures the notion that you're trying make a formalized standard without explicitly saying "this is the standard."

But I suspect it's also in part simply that Atwood and company never said in public "we are doing this." They just announced it as a fait accompli. Yes, two years ago Atwood and Gruber tweeted at one another briefly and Gruber said he wasn't interested in formalizing the spec. But that's not really an attempt at having a discussion, and it sure as hell isn't an announcement of a project.

I think a formalized spec for Markdown is a good thing. But the way this was handled was still kind of a dick move, and I don't think it had to have been.