Because that's how open source works. If you don't want for profit companies using code for free, then offer it under a license that states that.
This is interesting in terms of Github. They could pull the same thing and say only the porceline git client and MS approved clients can pull. After all it is their servers. The open source licenses are orthogonal to this and are between authors and users.
Back in the day if you caught someone hot-linking images from your web server it wasn't uncommon for admins to redirect abusive referrers to goatse etc. That usually got them to knock it off real quick.
Legally, he may be in the right (I'm not a lawyer and I'm not going to pretend like I can accurately predict the outcome of the ongoing lawsuit), but morally I think I can reasonably say that Matt is pretty squarely in the wrong when he's trying to abuse WP.org services to blackmail WP Engine out of 8% of their revenue.