In the Java Web Project the Compile on Save option works well, you can see this in action seeing the modified date of the .class files every time you modify classes, add new classes, etc.

The problem is that in a Java SE Project Compile on Save simply doesn't work, you modify classes, add new methods, modify existing, and the modification date of the .class files doesn't change

If you use tools like JRebel you can really feel this problem, I see that JRebel is guided by the modification date of .class files (produced by the compilation) in order to trigger reload of classes. NB doesn't compile classes, JRebel doesn't make its work, and users get really angry.

I send you an example:
Create an Ant Java Web project and a dependent Java SE Project. 
Both projects have the Compile on save option enabled.
In the Web project you have a Servlet called HelloServlet that invokes a class called HelloService located in the Java SE Project. Now do some changes to the servlet: Compile on Save works!, do some changes to the HelloService class, no Compile on save for you!