I will suggest one of many approaches to associate a Controller to an FXML file, I will suppose that you are using the fx:controller tag in your FXML file.
for the demonstration purpose, I will implement a demo app hosted on github with one button in the middle of the stage.

Demo__
     |___ App.java
     |___ AppModule.java
     |___ IController.java
     |___ Controller.java
     |___ InjectingFXMLLoader.java
     |___ fxml
              |__view.fxml
View.fxml
note that we refer to the interface in the fx:controller in the FXML file, and not to the implementation, so we can reuse the fxml view with other controllers implementing the interface.
<?xml version="1.0" encoding="UTF-8"?>
<?import java.lang.*?>
<?import java.util.*?>
<?import javafx.geometry.*?>
<?import javafx.scene.control.*?>
<?import javafx.scene.layout.*?>
<?import javafx.scene.paint.*?>
<BorderPane fx:id="root" xmlns:fx="http://javafx.com/fxml" fx:controller="org.tarrsalah.stackoverflow.guice.fx.IController" >
    <center>
        <HBox alignment="CENTER" prefHeight="-1.0" prefWidth="-1.0">
            <children>
                <Button fx:id="fx_print" alignment="CENTER" contentDisplay="CENTER" defaultButton="true" mnemonicParsing="false" onAction="#printButton" text="Print !" HBox.hgrow="ALWAYS" />
            </children>
            <BorderPane.margin>
                <Insets bottom="20.0" top="10.0" />
            </BorderPane.margin>
        </HBox>
    </center>
</BorderPane>
IController
an interface that the controller must implement , the printButton() to print a message to the screen , and getRoot() to get the Panel View.
import javafx.fxml.Initializable;
import javafx.scene.Parent;
public interface IController extends Initializable {
    public void printButton();  
    public Parent getRoot();
}
Controller
import java.net.URL;
import java.util.ResourceBundle;
import javafx.fxml.FXML;
import javafx.scene.Parent;
public class Controller implements IController {
    @FXML
    Parent root;
    public void initialize(URL url, ResourceBundle rb) {
    }
    public Parent getRoot() {
        return root;
    }
    public void printButton() {
        System.out.println("Hello Guice !!");
    }
}
InjectingFXMLLoader
a class with one static method that get a concrete implementation of a controller and 
URL of the FXML file and return the controller of the view.
import java.io.IOException;
import java.net.URL;
import javafx.fxml.FXMLLoader;
import javafx.util.Callback;
public class InjectingFXMLLoader {
    /**
     * 
     * @param <N>
     * @param injector
     * @return a controller injected within an FXML.
     */
    public static <N> N loadFXMLController(final N controller, URL url) throws IOException {
        FXMLLoader loader= new FXMLLoader();
        loader.setLocation(url);
        loader.setControllerFactory(new Callback<Class<?>, Object>() {
            public Object call(Class<?> p) {
                return controller;
            }
        });
        loader.load();
        return loader.getController();
    }
}
AppModule
in the  guice module , we use the InjectingFXMLLoader class to associate a concrete implementation of the controller with the corresponding FXML file. using a @Provides method.
import com.google.inject.AbstractModule;
import com.google.inject.Provides;
import java.io.IOException;
public class AppModule extends AbstractModule {
    @Override
    protected void configure() {
    }
    /**
     *
     * @return IController
     * @throws IOException
     */
    @Provides
    public IController getIController() throws IOException {
        return InjectingFXMLLoader.loadFXMLController(new Controller(), getClass().getClassLoader().getResource("fxml/view.fxml"));
    }
}
App
the main class that show the view
import com.google.inject.Guice;
import javafx.application.Application;
import javafx.scene.SceneBuilder;
import javafx.stage.Stage;
public class App extends Application {
    public static void main(String[] args) {
        launch(args);
    }
    @Override
    public void start(Stage stage) throws Exception {
        stage.setScene(SceneBuilder
                .create()
                .root(Guice.createInjector(new AppModule()).getInstance(IController.class).getRoot())
                .height(160)
                .width(200)
                .build());
        stage.show();
    }
}