I'm with Vash21 on this one; intentionally or not, WWE is giving kind of a mixed role to the NXT guys right now. At first they were a totally heel faction, for sure, taking out pretty much exclusively good guys--Cena and Bret--as well as non-wrestlers--poor Justin Roberts, haha.
Now, as others have stated, they're focusing on Sheamus, who is definitely a heel. They're also focusing on McMahon, who I think was definitely characterized as a heel on last night's RAW... He seemed to take pleasure in firing Bret, he was sucking up the the NXT heels, he asked for a round of applause for himself. That's totally ol' power-hungry Mr. McMahon.
So the mixed reaction of the crowd is to be expected... they're taking out faces and heels now, so how else would you expect the crowd to respond, other than with mixed reactions? And personally, I think this is a cool thing to happen; they're becoming a sort of tweener group, who'll take out anyone in their path--WWE might be doing this to test the waters to see how fans respond to these guys as faces and heels, too.