He's belittling the political stance of code.org as represented by its marketing.
He's not saying "don't teach kids how to program", he's saying "we're teaching kids how to program for the wrong reasons". The implication is, if you're teaching it for the wrong reasons, we're not doing the best we could for the kids.
That's a perfectly valid thing to say, independently of the good intentions and sincere efforts of all the people involved.