The detective's strange investigative technique bothered me as well. It doesn't work very well in the context of the story. I can think of a couple of ways it could be made believable, but would still be quite unorthodox.
The controversy surrounds his outrageous claims that the book isn't a fiction but a real historical work.
Further, Brown makes outrageous mistakes on simple facts. It's really dumb, boring, reguritated pulp fiction. Eco's book on Focucault's pendulum was a well written satire on the whole deep tinfoil hat conspiracy genre.
Supposedly his next book will be on the Masons.
In any case, Brown's books reminds me of Hanna Ardent's sardonic comment that 19th century historgraphy was obsessed with the backstairs of history with Jesuits, freemasons, Jews and other manipulating history from anonymous rooms in the back alleys of big cities.
I'm glad I'm not the only one who found Brown's technique offputting. Eco toys with the detective genre in both Name of the Rose (the detective monk is William of Baskerville) and Foucault's Pendulum (the narrator describes himself as a Sam Spade of culture), and I assumed that Brown would adhred to the conventions of the detective story as well. It was really offputting. I'll still get around to reading it though.
That's a great quote from Arendt -- for a while, I spent a fair amount of time digging through that sort of book (it extended beyond the 19th Century; see, for example, Nesta Webster, who wrote in the mid-1920s that while the Protocols may be a forgery, they describe a conspiracy that's all too real). I think one of the best passages in Foucault's Pendulum is the one in which Casuabon describes himself as a sanitarium doctor, viewing his patients' manias with indulgent bemusement, who ends up a patient himself.
Eco's is the ultimate anodyne for the silliness, but before him I read quite a lot of rosicrucian/neognostic/kabbalistic nuttiness and speculation, including the interesting "Fingerprints of the Gods" subgenere and the just plain whack Robert Anton Wilson novels.
My own dislike of Brown's book is that it has otherwise reasonable people, who never before braved those nutty halls I once explored, suddenly spouting as new-found ah-ha's some amazingly sloppy rehashings of the pseudo-history that is grist for that crazy old mill. Because they haven't heard it all before, it seems like New Truth, and yet compared to all the "Truth" floating in the backwaters of Illuminoidia, it's pretty cheap stuff indeed. Those who know me as a Bible scholar ask me questions, and I must admit it exhausts me trying to find a place to start that won't lead to too long and ridiculous a journy for all parties.
You want a real-life, no-nuttiness-added example of centuries-long religious censorship, try the more mundane (yet still wonderfully fascinating) Michael Servetus on for size.