The tutorial you have mentioned focus on creating RESTful Webservices with Java. It aims at distributed systems, where a client can make requests to a server. I think the tutorial is very helpful for that matter.
On the other hand, you seem to be searching for a tutorial that helps you creating a web application that can save/retrieve data to/from a database. You can find one, for example, in http://zetcode.com/tutorials/jeetutorials/mysqldatabase/
Then, for web clients, you have different alternatives, such as GWT or JSF. Also, for the persistence layer you might want to check Hibernate or JPA.
Relatively to Tomcat, it implements the Java Servlet and the JavaServer Pages (JSP) specifications from Sun Microsystems, and provides a "pure Java" HTTP web server environment for Java code to run. In short, Tomcat is the place where you deploy and run your Java web application; like you deploy a PHP application in Apache (with PHP installed).