I guess it's common sense that bookstore chains don't--and just can't--carry every book that's published. They have a limited amount of space and publishers just keep churning out hundreds of thousands of new books every year. Still, when you have a track record, a good sales rep who can get a meeting with the buyers, and a dominance in your niche, most of the time they will give most of the books on your list a shot, in varying degrees. It's just the few times that they don't that really sting. (I'm trying to take it less personally, really, I am.)
Yesterday MediaBistro pointed me in the direction of this article written by Wiley science fiction marketing manager Andrew Wheeler about a recent trend toward more "skipping," which is what they call it when the chain says "no, thank you" to carrying a book. In it he gives some great inside info on how the trade buying model works.
What do you do if you get skipped? Amazon will list just about any book, so optimize your listing online and drive all of your customers there to buy it. (This is just one of the many reasons I like Amazon.)