This is one way which perfectly worked to remove index.php from CI URLs for me. 

• .htaccess file: create a .htaccess file and put this in codeigniter root folder. 
• write the following code in this file: 

<IfModule mod_rewrite.c>

RewriteEngine On

RewriteBase /ci

#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]

#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

#This last condition enables access to the images and css folders, and the robots.txt file

#Submitted by Michael Radlmaier (mradlmaier)

RewriteCond $1 !^(index\.php|images|robots\.txt|css)

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>    

• rename ‘ci’ to your CI installation root folder.
• enable mod_rewrite on apache (httpd.conf)
• modify $config['index_page'] = 'index.php'; to $config['index_page'] = '';

And this works perfectly for me. You can find this article here too.