Remove index.php from CodeIgniter URLs

Where did you get that the index page should be blank? Do you mean index.php? It should be something like this:

<?php
/*
|---------------------------------------------------------------
| PHP ERROR REPORTING LEVEL
|---------------------------------------------------------------
|
| By default CI runs with error reporting set to ALL.  For security
| reasons you are encouraged to change this when your site goes live.
| For more info visit:  http://www.php.net/error_reporting
|
*/
        error_reporting(0);
//      ini_set("display_errors", "on");

/*
|---------------------------------------------------------------
| SYSTEM FOLDER NAME
|---------------------------------------------------------------
|
| This variable must contain the name of your "system" folder.
| Include the path if the folder is not in the same  directory
| as this file.
|
| NO TRAILING SLASH!
|
*/
        $system_folder = "system";

/*
|---------------------------------------------------------------
| APPLICATION FOLDER NAME
|---------------------------------------------------------------
|
| If you want this front controller to use a different "application"
| folder then the default one you can set its name here. The folder
| can also be renamed or relocated anywhere on your server.
| For more info please see the user guide:
| http://codeigniter.com/user_guide/general/managing_apps.html
|
|
| NO TRAILING SLASH!
|
*/
        $application_folder = "application";

/*
|===============================================================
| END OF USER CONFIGURABLE SETTINGS
|===============================================================
*/


/*
|---------------------------------------------------------------
| SET THE SERVER PATH
|---------------------------------------------------------------
|
| Let's attempt to determine the full-server path to the "system"
| folder in order to reduce the possibility of path problems.
| Note: We only attempt this if the user hasn't specified a
| full server path.
|
*/
if (strpos($system_folder, '/') === FALSE)
{
        if (function_exists('realpath') AND @realpath(dirname(__FILE__)) !== FALSE)
        {
                $system_folder = realpath(dirname(__FILE__)).'/'.$system_folder;
        }
}
else
{
        // Swap directory separators to Unix style for consistency
        $system_folder = str_replace("\\", "/", $system_folder);
}

/*
|---------------------------------------------------------------
| DEFINE APPLICATION CONSTANTS
|---------------------------------------------------------------
|
| EXT           - The file extension.  Typically ".php"
| FCPATH        - The full server path to THIS file
| SELF          - The name of THIS file (typically "index.php")
| BASEPATH      - The full server path to the "system" folder
| APPPATH       - The full server path to the "application" folder
| MEDIAPATH - The full server path to the "media" folder
*/
define('EXT', '.'.pathinfo(__FILE__, PATHINFO_EXTENSION));
define('FCPATH', __FILE__);
define('SELF', pathinfo(__FILE__, PATHINFO_BASENAME));
define('BASEPATH', $system_folder.'/');
define('MEDIAPATH', dirname(__FILE__).'/media');

if (is_dir($application_folder))
{
        define('APPPATH', $application_folder.'/');
}
else
{
        if ($application_folder == '')
        {
                $application_folder = 'application';
        }

        define('APPPATH', BASEPATH.$application_folder.'/');
}

/*
|---------------------------------------------------------------
| LOAD THE FRONT CONTROLLER
|---------------------------------------------------------------
|
| And away we go...
|
*/
require_once BASEPATH.'codeigniter/CodeIgniter'.EXT;

/* End of file index.php */
/* Location: ./index.php */

Mind you I randomly grabbed this from one of our CI projects so it might be customized - I don't really remember - but it is definitely not blank.

Also, the config:

$config['uri_protocol']="REQUEST_URI"; 

and htaccess:

<IfModule mod_rewrite.c>
    RewriteEngine On
    RewriteBase /

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

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

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