Codeigniter URL rewrite to remove index.php

First of all, i have tried the suggestion specified in here:

• CodeIgniter removing index.php not working
• codeignitor: Remove index.php not working
• CodeIgniter .htaccess index.php rewrite not working on user directory
• How to remove "index.php" in codeigniter's path
• https://ellislab.com/expressionengine/user-guide/urls/remove_index.php.html
• Rewriterule for CodeIgniter not working

I am trying to remove the infamous index.php on the address bar.

This is my current configuration:

In my /etc/apache2/sites-available/my.website.com.conf file i put this:

<Directory /path/to/root/directory/>
   AllowOverride All
   Order allow,deny
   Allow from all
</Directory>

In my /etc/apache2/apache2.conf file, i put this:

<Directory /path/to/root>
        Options Indexes FollowSymLinks
        AllowOverride None
        Require all granted
</Directory>

In my codeigniter root directory (same dir with index.php), i have a .htaccess like this:

<IfModule mod_rewrite>
        RewriteEngine On
        RewriteBase /

        #Removes access to the system folder by users.
        #Additionally this will allow you to create a System.php controller,
        #previously this would not have been possible.
        #'system' can be replaced if you have renamed your system folder.

        RewriteCond %{REQUEST_URI} ^system.*
        RewriteRule ^(.*)$ /index.php?/$1 [L]

        #When your application folder isn't in the system folder
        #This snippet prevents user access to the application folder
        #Submitted by: Fabdrol
        #Rename 'application' to your applications folder name.
        RewriteCond %{REQUEST_URI} ^application.*
        RewriteRule ^(.*)$ /index.php?/$1 [L]

        #Checks to see if the user is attempting to access a valid file,
        #such as an image or css document, if this isn't true it sends the
        #request to index.php

        RewriteCond %{REQUEST_FILENAME} !-f
        RewriteCond %{REQUEST_FILENAME} !-d
        RewriteRule ^(.*)$ index.php?/$1 [L]
</ifmodule>

<IfModule !mod_rewrite.c>
        # If we don't have mod_rewrite installed, all 404's
        # can be sent to index.php, and everything works as normal.
        # Submitted by: ElliotHaughin

        ErrorDocument 404 /index.php
</ifmodule>

And finally, my application/config/config.php:

$config['base_url'] = 'http://my.website.com';
$config['index_page'] = '';
$config['uri_protocol'] = 'REQUEST_URI';

When i tested the above config on my local PC (running Ubuntu 14.04) it works just fine. However when i try to replicate the config on my server (running Ubuntu 14.04), somehow it does not work.

Doing this:

• http://my.website.com/ << Shows default Codeigniter welcome page

• http://my.website.com/controller_name/ << Shows :

  Not Found The requested URL /login was not found on this server. Apache/2.4.7 (Ubuntu) Server at my.website.com Port 80

• http://my.website.com/index.php/controller_name << shows the page, however URL to static files (i.e JS/CSS/images) are not properly fetched, since printing this:

    <link rel="stylesheet" href="assets/styles/material-design-icons.css" type="text/css" />
    <link rel="stylesheet" href="assets/styles/font.css" type="text/css" />
    <link rel="stylesheet" href="assets/styles/app.css" type="text/css" />
  

would append index.php when seen from source code inspector.

Am i missing something here? Can someone point me to the right direction?

Thanks.

EDIT #1 Below is my folder structure

EDIT #2 I can confirm that mod_rewrite is enabled