I'm confused about the differences between objects and the primitive data types, such as int and boolean.
The primitive types (byte, short, int, long, float, double, boolean, and char) represent the smallest things in the language. They are not objects, although in many ways they can be handled like objects: They can be assigned to variables and passed in and out of methods. Most of the operations that work exclusively on objects, however, will not work with primitive types.
Objects are instances of classes and, as such, are usually much more complex data types than simple numbers and characters, often containing numbers and characters as instance or class variables.
The length() and charAt() methods in Listing 3.3 don't appear to make sense. If length() says that a string is 36 characters long, shouldn't the characters be numbered from 1 to 36 when charAt() is used to display characters in the string?
The two methods look at strings a little differently. The length() method counts the characters in the string, with the first character counting as 1, the second as 2, and so on. The string "Charlie Brown" has 13 characters. The charAt() method considers the first character in the string to be located at position number 0. This is the same numbering system used with array elements in Java. The string Charlie Brown has characters ranging from position 0 (the letter "C") to position 12 (the letter "n").
No pointers in Java? If you don't have pointers, how are you supposed to do something like linked lists, where you have a pointer from one node to another so you can traverse them?
It's untrue to say Java has no pointers at all; it just has no explicit pointers. Object references are, effectively, pointers. To create something like a linked list, you would create a class called Node, which would have an instance variable also of type Node. To link together node objects, assign a node object to the instance variable of the object immediately before it in the list. Because object references are pointers, linked lists set up this way behave as you would expect them to.