user.routes.js

var express     = require('express');
var router      = express.Router();
var jwt         = require('jsonwebtoken');
var bcrypt      = require('bcryptjs');
var hash        = 'superSecret';
var config      = require('../config/database');

User = require('../models/user.model.js');

// Create new User
router.post('/', function(req, res){
  var email = req.body.email;
  var password = req.body.password;
  var user = new User({
    email: email,
    password: password
  });
  // Pre hook will take care of password creation
  return user.save()
  .then(function(user) {
    // return user successful and token
    console.log('get ready to prepare the token');
  });
});

You need to make an instance of a user you cannot call the save method on the model

 var express     = require('express');
 var router      = express.Router();
 var jwt         = require('jsonwebtoken'); 
 var bcrypt      = require('bcryptjs');
 var hash        = 'superSecret';
 var config      = require('../config/database');

 User = require('../models/user.model.js');

  // Create new User
  router.post('/', function(req, res){
      var { password, email } = req.body;
      var user = new User({
        name: name,
        password: password
      });
      // Pre hook will take care of password creation
      return user.save()
      .then(function(user) {
        console.log('routes user', user);
        return res.status(201).json({user, message: 'User was succesfully created'});
      });
    });

Ok so passing a user object now back into the Model