Apple have been in touch with PhoneGap devs since and clarified the matter; there's a good blog post here regarding that: http://nachbaur.com/blog/updates-on-apple-phonegap
Since then Apple have had a much more informed stance towards PhoneGap and have approved lots of apps using the framework (there's a list on the PhoneGap site).
*full disclosure - I work for Nitobi, who sponsor PhoneGap's development. Though the original link suggests using PhoneGap in its preface, there are competing platforms, such as Rhodes and Appcelerator, that also get through to the App Store.
Edit:
Please see my reply to the comment below.
Also, this is from the preface of the book:
Fortunately, there is an alternative. You can build a web app using open source, standards based web technologies (jQuery and jQTouch, in particular), release it as a web app, and debug and test it under load with real users. Once you are ready to rock, you can use PhoneGap to convert your web app to a native iPhone app and submit to the App Store. If it is ultimately rejected, you aren’t dead in your tracks because you can still offer the web app. If it is approved, great! You can then start adding features that enhance your web app by taking advantage of the unique hardware features available on the device. Sounds like the best of both worlds, right?
So, the step to wrap your app with something like PhoneGap is only needed if you want to sell your app on the AppStore. You can try to submit and then, if it is approved, you may add more hardware dependant features (which aren't covered at all by this book).
You can do that via Javascript running through an app (Phonegap is great for this), but can't do that via a web app.
Or the official Apple documentation (http://developer.apple.com/safari/)?
http://developer.apple.com/safari/library/samplecode/iPhoneO...
http://developer.apple.com/safari/library/documentation/Appl...
Edit: where in the book did you see how to use geolocation, vibration or any other feature which is not available with a web app developed for mobilesafari?