This is a very new age concept where you as the reader are supposed to be confused as to who the hero or villains in the story are. they tried this with wheel of time series and was somewhat unconvincing.
This is why I dislike anti hero 90's ish type characters and I love the original star wars trilogy because the bad guys and good guys are so well defined. That might not be in vogue with post 911 darkness end of the world shit but so be it.
The prequels sucked and were a downer because we were supposed to root for the dark anti hero.
tolkien's hero's and villains had a very thin line between them because a christian writer would know about the fall of man and sin. although no such words were used in his books sauron and the devil are pretty much the same and the ring as the tempter. Frodo was saved by Grace because like Bilbo he pitied Gollum and forgave him.