I belong to the category of developers that used Prototype in the past. The funny thing is though that both libraries offer almost identical sets of functionality. You may ask why did I decide to go with jQuery?
I like its innovative way of querying for page elements and to iterated over them, allowing you to often accomplish multiple tasks with just one line of code. jQuery in Action starts out explaining those core concepts of jQuery in the first 3 chapters of the book - allowing to query for page elements using the CSS syntax, how to manipulate page elements as well as how to work with collections of elements. The book does a very good job explaining those aspects of jQuery combined with many useful examples.
What also drove me to jQuery was the fact that it has a plug-in mechanism that allows you to either use additional third party add-ons or to write your own plug-ins by still adhering to the spirit of jQuery.
I guess this is a drawback writing a book about a subject that is evolving with the speed of light.
Nevertheless, despite all my critical remarks, I think that jQuery in Action is an excellent book that will help you learn and understand jQuery. I certainly enjoyed reading the book.