The following code fragment:

            root = new Group();
            Rectangle rect = new Rectangle( 10, 10, 100, 100);
            rect.setFill( Color.RED);
            rect.setStroke(Color.BLACK);
            rect.setStrokeWidth(2);
            root.getChildren().add( rect);

            Line line = new Line( 1, 1, 150, 100);
            line.setStroke( Color.BLACK);
            line.setStrokeWidth(2);
            
            root.getChildren().add( line);

            Scale scale = new Scale( 5, 5);
            root.getTransforms().add(scale);

        // Create and show the stage
        stage.setWidth(800);
        stage.setHeight(600);
        Scene scene = new Scene(root);
        stage.setScene(scene);
        stage.setVisible(true);

produces the scene visible in the attached screenshot. Please note that the rectangle's stroke width is, quite correctly, 10px (2 x 5) whereas the line stroke width is only 2px, as if there was no scale transformation at all.