I haven't read the book. I'm working on it. But, I have seen the movie. Here are some thoughts:
Undoubtedly, it is fiction. It twists history to make a point. Mostly Brown is trying for good fiction, but I think he's scoring some political points in there as well. I don't think that's much different than the authors of Left Behind or other evangelical, apocalyptic fiction, though. They twist scripture to fit their ideological and political points of view.
I think one of the best things that could come from this book/movie is a resurgent interest in church history. Most Christians I know don't really have a solid understanding of church history. And that makes sense--it can often be a big shock, to see the power struggles, the politics, the way that things we take for granted today were socially constructed. But I think challenging and learning is part of faith. All education, good education at least, gets at the root of how and why we "know" what we "know." It always involves a good bit of shock. All good education challenges our preconceived notions, questions received wisdom. We can't sit in a bubble and have people tell us what we want to hear. How does that grow faith? How does that grow a person?
While much of Brown's "history" is not history at all (it's fiction, people!!), my hope is that it will cause interest in church history, the formation of doctrine and the canon, etc. Maybe it will cause us to reexamine our notions of "Jesus" and how he has been constructed historically. Brown's version may not be accurate, but neither is the Jesus that is dominant in today's culture. We have the filter of churches, authors, commentators, and culture telling us what Jesus should be like. Who needs the bible at all, really?
My fear is that those who might most benefit from the questioning/thinking process that could be started from this book/movie are the very ones who won't go to see it. But that's always how it is, isn't it?