They were pretty true to the spirit of the books, but there were a few changes that probably have the hardcore geeks up in arms. First, the Liam Neeson character (although superb) is definately not a part of the original comic origins of Batman. Miller did have Wayne travel to Tibet to learn a secret fighting style, but I don't recall Raja Ghule in any of the books.
Secondly, in the new film Wayne isn't a science nerd at all. In fact, he pretty much doesn't understand a word Fox says about how the gadgets work. In the comics Bruce Wayne has a brilliant scientific mind.
Also, the Holmes character is invented just for this film. No Vicki Vale for Wayne here.
Of course, none of this matters at all to me. I loved the flick. Too often a movie based on a comic is criticized for deviatings from the books. But comics and films are very different art forms, and what works in one may not work in the others. For example, I can't fathom how LotR was criticized for omitting large sections of the book- even with what they did include the extended series runs 12 hours for three films!
IMOHO, Batman Begins is just about perfect considering the source material. It's almost as good as Spiderman 2, which I consider the best comic book based film in history.
