The book is very historically inaccurate. Any historian will tell you its pure fiction. Even Dan Brown's "Theory" is simply discustingly inaccurate with history. It's not a theory, it's a piece of fiction. People who take it as fact are either idiots or just haven't learned history.
One of the problems is that the church is afraid people will take it literally.
The problem with the book is that People DO take it serious. Not that they believe that theory, but in the book, the Catholic Sect Opus Dei are portrayed as murderous, machiavellian religious criminals. People read the book and actually belive that the Opus Dei are murderers, when in fact, they're one of the most ethical sects of catholism. A survey showed that something like 40% of Da Vinci Code readers belived that the Opus Dei had murdered people. About 3% who did not read the book did.
The book is a whole lot of biased and dangerous propaganda. The Church has the right to defend themselves against baseless defamation.