The definition (of bootstrapping) from Wikipedia has more flair to it than I can probably give this article, but nonetheless bootstrapping is an incredibly important part of a PHP web application. It is the ignition, the launch-pad, the booster rockets, and even the safety gear for our trip through PHP Best Practices. Without a well designed bootstrap, our application will never get off the ground.
The general idea behind the bootstrapping is forcing all of the requests to a domain to be funneled through a central script and branching out from there. They talk about how to use Rewrite rules to accomplish this and how to set the setup. He finishes the post off by bringing it back to the layout of the application, pointing out where it fits in.