That's an interesting debate. Of course, it becomes difficult to measure such things, but here in the UK at least, I've not met a single person who thought the cumulative effect of the first two Godfather films was to glamourise organised crime. Rather, they are compelling Shakespearean dramas gripplingly and entertainingly exploring darker aspects of the human condition, as well as providing a modicum of comment on the dark side of the American Dream.
Another interesting case in point: Steven Spielberg's Munich. I thought this was a superb film at every level, but when it was released, it was decried in many quarters as either too pro-Palestinian or too pro-Israeli. Spielberg felt the need to clarify his intentions with an introduction on the DVD. As I listened to what he had to say, my response was slightly "Well, duh" because everything he'd intended I'd picked up from watching the film in the cinema. It was inherent. All that said, the very fact that he felt the need to clarify his intentions begs the question: Did he fail as an artist if what he meant to say was so widely misunderstood? It appeared I was in a minority in understanding his message.
As I said, an interesting debate. :)