The first is that teams are running it less, especially the two big teams in Washington and Carolina. So read option attempts are down, mostly because of the increased worry of injuries to their QB's.
The second is defensive coordinators had a whole off-season to watch tons of read option plays and see what worked in college. While the read option is new to the NFL, it isn't new to college and reportedly NFL defensive coordinators had a lot of film sessions with college coaches to help them learn to beat it. I also think fans don't give enough credit to defensive coordinators who have spent their careers learning how to stop offenses. Similarly how Chip Kelly's offense was supposedly supposed to change the NFL, in reality teams caught on after week 1 once they realized that his offense, like the read option in general, is fairly basic, it's just based on one aspect of the play, if you can control the rest of the field, it doesn't matter what the QB and RB do.
I expect the read option to still exist in the NFL for the foreseeable future, but I don't expect it to be a vital part of any offense besides Chip Kelly's (until Vick gets hurt, then he'll run a normal offense).More questions on 2013-14 NFL Season: