I think we're talking about two different rulings. Last December the FCC issued a rule. I believe the new rule allows all cable companies to encrypt anything they want to.
But before that, New York Cablevision had requested a waiver from the earlier rule, which required them to keep all the basic channels unscrambled. The FCC gave them a full waiver for NYC and a partial waiver for suburbs. The partial waiver allowed Cablevision to encrypt everything except local OTA channels in the suburbs.
The new December rule would presumably let Cablevision encrypt the locals even in the suburbs now, but it sounds as if they haven't done so (at least, not yet).
So far, only NYC and parts of Minneapolis have confirmed the loss of clear local channels on cable. I'm still trying to find out about Houston.