Edit: Sorry for the re-post but I think some things have to be clarified. Also some spoilers.
While satiric gems like Thank You For Smoking and Dr. Horrible's Sing-Along Blog put audiences in the eyes of the villain and subvert the distinctions of good and evil, there is a larger and more disturbing trend among the cinema mainstream in empathizing with the villain which seems to be done for the opposite purpose.
Decades ago, the antagonist was much like a James Bond villain, ominously in the background and if he was seen at all, it was nefariously plotting against our protagonist.
Somewhere along the lines, that seemed to change. Now villains are no longer powerful people who hide and plot, they are often just as, if not more desperate then the hero in getting what they want. Just take the modern versions of James Bond, the films with villains so archetypal that the very idea of a "Bond villain" creates a vivid image in one's head. In Casino Royale, the villain is a terrorist financier who has troubling making ends meet with assassins threatening to kill him just as much as they do Bond. Not exactly a Dr. No-type character threatening the end of the world.
A good example of this can be seen in the Bourne series. While the first film was rather bold in presenting a villainous government pursuing Bourne (especially since it was released a year after 9/11) what's odd are the two movies that followed. With the second and third film, not only does the audience spend more time with the antagonistic government but Bourne's enemies become weaker with each film.
In fact, I'm willing to bet that by The Bourne Ultimatum we spend more time with the government then with Bourne. Indeed it should seem odd that people would root against an organization that becomes weaker and weaker and more difficult to manage when an unstoppable killer is trying to undermine it.
But isn't this a good thing? After all, what can be wrong with adding empathy and depth to the people we're supposed to root against? Doesn't this increase our understanding of the villain and thus fulfill our liberal desire at rehabilitation?
Well the problem with this logic is that, while on the surface this may look like a post-modernist attempt to subvert the genre with a "realistic" perspective (and thus to make people think critically) it does the exact opposite: it reinforces the simple narrative of a morality play but now asks the audience to see past the antagonists' complexity to condemn them.
Thus "realism" is always bound within the structure of a story. For instance, it would be silly to ask for a "more realistic" propaganda film, the medium is reinforced, not subverted from it. Indeed, Zizek made a similar conclusion regarding so-called "anti-war" films.
Mainstream Hollywood films are not often Shakespearean tragedies where all the parties are guilty, there are distinct "bad guys" that are made to be held accountable for their crimes while heroes are to be rewarded.
Just take the recent Avengers film, to say that the Avengers are just as guilty as Loki would be silly, it is a clear morality play of good versus evil. But the effect of having Loki be a somewhat sympathetic character is to force yourself to know that, whatever his circumstances, he is still a "bad guy" and needs to be punished for what he did (although to be fair, Joss Whedon was probably aware of this, which is why Loki is only arrested at the end).
Taken to its extremes, one can easily imagine a morality tale situation where a "bad guy" who robs a store to support his family is stopped by a "good guy" and that, no matter what the bad guy's circumstances, no matter what social circumstances exist, we must look past them and fulfill a regressive Victorian urge to punish.
My hypothesis is that this is effect of the films, that having a "realistic" morality play which makes you feel for the villains, is akin to having a "realistic" propaganda film.
It's only more effective at hardening people to the circumstances of the villain and thus becomes a very subtle form of victim blaming since, in the end, the story calls for a punishment over the empathy we feel for them.
It's why, in the structure of a morality play, the truly subversive thing to do is not to have more empathy for the villain but less. It's why books and films like the Millennium series doesn't try to empathize with the villains, we know full well what they are doing is wrong.
Our job shouldn't be to increase the "realism" of morality plays, it's to subvert the very structure of them.