Why be mad at the fans?
See, I'd understand your point if the fans were constantly chanting "boring" or the constantly annoying "what?", but they were clearly pushing chants that had something to do with the angle at hand. It seems like the whole thing goes back to "is it ok to cheer for a heel?", and the answer is indefinitely yes. Cheering for a heel is basically rooting for the bad guy in a movie, book, comic, or any other TV show. It happens quite often really, and should be accepted whether you're at home thinking it or in a stadium of fans chanting it.
As to the mixed reactions (boos and cheers) that the NXT guys got, I really didn't expect anything less. Think about it, in the past 24 hours, they attacked the top face of the company (one that gets mixed reactions himself), cost him the title which was then won by a hated heel, but then they attacked and verbally mocked the heel as well. From the perspective of a fan, you want to boo them for some of there actions, but if you really are against Sheamus or Cena, you want to cheer them too.
I think John Morrison said it well on NXT a few weeks ago. Some people cheer, some people boo, but all that matters is you get a reaction. The NXT Season 1 guys were relatively unknown to the RAW audience, but are now viewed as threats to the top guys of the company. More so, the fans (be it because of Daniel Bryan or because of the angle) have found reasons to cheer or boo during the NXT segments. Regardless of whether or not it plays along to the angle, the angle itself has gotten a reaction, which is exactly what it was supposed to do.
As for the Daniel Bryan chants specifically, I believe they will die out a bit after a while, but are likely going to have some kind of effect on the WWE management. Someone already compared this to the Matt Hardy thing back in 2005, and I agree. Here you have someone built up by the company (although not completely, but that shouldn't matter) that was released under unfortunate circumstances, but yet he still has ties to a current angle and is incredibly over despite his absence. If and when Bryan is able to return to the WWE, the fan reaction will be months in the making.
So, I really can't see a major downside to the fan reaction. At no point in time would I say they are ruining the angle at all. People can cheer and boo whoever they wish, and I for one am actually satisfied with the fan response to this angle.
I'd much rather have a group of fans cheering the heels and booing the faces than a dead crowd.