I had the same exact problem as you, unfortunately the way Wiredesignz created the extension it requires that the path start with the module name itself if you put the routes file inside the module itself. That is the only way it will look at the routes file if it is placed inside a module. With that said it already knows the module name at that point, so you need to simply specify the controller and method that you want it to route to. So in your routes.php file inside of your module config directory, if you put this:
$route['yourmodule/some-route'] = "yourcontroller/yourmethod";
or in other words:
$route['user'] = 'user/login';
That would work I believe. However I still wanted more than this. I wanted to be able to use routes that may or may not have the module name. Due to this I had to extend the module to make this happen, and you can find the work I did here if this helps:
https://github.com/brianwozeniak/codeigniter-modular-extensions-hmvc
This would then allow you to use the route you wanted such as:
$route['login'] = 'user/login';
Even with that routes.php placed inside the module's config directory.