Presumably, he's annoyed that he distributed a piece of software under the terms of the GPL, and others extended it and sold those extensions under proprietary terms. If this was ffmpeg, we wouldn't even have to wonder about it.
To expand on your comment - Matt Mullenweg is often quick to point out that WordPress itself came into being by forking a GPL'd abandonware project. It's because of this that I think he genuinely wants to ensure users of the software have the same opportunities he has had.
Also, regarding the marketplace surrounding WordPress, WooThemes distribute their themes under the GPL and per Andrew Warner's interview with co-founder Adii Pienaar (http://mixergy.com/woothemes-adriaan-pienaar/) they make $2+ million a year and have had some of their code incorporated back into WordPress by Automattic. This should assuage any fears about GPL themes being commercially viable and of Automattic taking a dislike to others making money off of WordPress.
As a big fan of the GPL I don't mean to come across as totally flippant. However, I just don't see a problem with people selling themes.
In a hurry, not enough skills, buy a theme. Skilled with the time to make your own, then roll your own.
You have a choice, you are not compelled to pay for a theme if you don't want to. The software will continue to work regardless.
Unless there is some kind of legal stalking horse that could affect the GPL, I don't see the point of all the fuss.
I use both Wordpress and Joomla and I see the same kind of thriving ecosystem around both projects. Commercial and non-commercial plugins and themes for both. Seems like a good thing to me and I don't see why it has to be an either/or situation.
If I am missing something then I would like to hear it.
There is no problem with selling themes. What may be a problem is distributing a theme under another license.
I think it's unlikely they'll do anything about this as legal action would be detrimental to their community; meaning that this won't be decided unless someone who receives a non-GPL'd theme contests it. This doesn't preclude Automattic/Matt from stating their view and raising a bit of a fuss as you put it in the interim.
To be clear - I'm neither a fan of the GPL, a lawyer or a WordPress user so I don't know whether Automattic is in the right and I'm indifferent as to whether or not they are.