I've read this a few times to my children. The illustrations are amazing, very panoramic, lovingly imagined, carefully detailed. The story, however, always strikes me as oddly incomplete. It has a goal, a sentiment, which is fine, but I'm always left scratching my head a little bit. This Polar Express travels all night bringing masses of children to the North Pole so Santa can choose one to give a first Christmas gift to? That alone doesn't make much sense to me. I refuse to believe that that train isn't full of mostly disappointed children on the return trip. Then there's a mini crisis for a couple of pages near the end when the first Christmas gift is briefly lost. I'm still not sure how that fits in or why it matters.
Anyway, the message about truly believing in Santa (and maybe the spirit of Christmas) and the gorgeous illustrations seem to be enough for many people to gloss over those things.