JavaFX app in System Tray

Wrap the code in the actionListener which calls back to JavaFX in Platform.runLater. This will execute the code which interfaces with the JavaFX system on the JavaFX application thread rather than trying to do it on the Swing event thread (which is what is causing you issues).

For example:

ActionListener listenerTray = new ActionListener() {                
  @Override public void actionPerformed(java.awt.event.ActionEvent event) {
    Platform.runLater(new Runnable() {
      @Override public void run() {
        primaryStage.hide();
      }
    });
  }                   
};            

By default the application will shutdown when it's last window is hidden. To override this default behaviour, invoke Platform.setImplicitExit(false) before you show the first application Stage. You will then need to explicitly call Platform.exit() when you need the application to really shutdown.

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I created a demo for using the AWT system tray within a JavaFX application.

The system tray is not supported in JavaFX yet. You could track the progress on this task under the following JIRA issue: https://bugs.openjdk.java.net/browse/JDK-8090475
The issue also provides a workaround, which could be used in JavaFX 8 to get the basic support.

The feature is not planned for JavaFX 8, so it might be released in one of the following updates or even in JavaFX 9.

You should only modify the javafx classes on the javafx thread, the listeners on the tray icon are likely to be running on the swing thread. You can do this by posting a runnable to Platform#runLater like so:

Platform.runLater(new Runnable() {
    public void run() {
        primaryStage.hide();
    }
});