Do you really think he is empowered to make decisions?
Last week after Fran mentioned we would see more than one QB this week someone asked Nunz who was going to start.  He responded with “that’s not for me to say”.  He didn’t say “you’ll see Friday night” or “a decision hasn’t been made yet”.  His response tells me, even though he’s the QB coach, he is not the one deciding who plays.  Makes me wonder if he agrees with the decisions that have been made. 
Last night was bad in so many ways (bad for the QB’s, bad for the WRs who can’t get a ball thrown to them), but it was also bad for Nunz cause people will ask why he doesn’t have the QB’s ready to play.  His reputation as a QB coach will take a hit.  Regardless of what Fran may say, it doesn’t look like Fran trusts Nunz (or any of his assistants).  I’ll be surprised if Nunz is back after the season.