JavaFX script (the .fx files) was created for the now obsolete and unsupported JavaFX 1.x distribution. Support for JavaFX 1.x and .fx scripts was dropped from NetBeans after the NetBeans 6.9 release. Use of JavaFX script and JavaFX 1.x is not recommended.
JavaFX 2.x+ is a complete rewrite of the JavaFX system in Java. JavaFX 2.x also includes an XML based markup language named FXML. All major JavaFX IDEs currently support JavaFX 2.x development based on .java and .fxml files.
Use of JavaFX 2.x+ is recommended.
If you wish to use a scripting language for JavaFX 2.x, you can use JrubyFX, GroovyFX, JavaScript, etc. I recommend learning JavaFX programming with the plain Java API before learning JavaFX programming with a scripting language.