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Options +FollowSymLinks 
Options -Indexes 
DirectoryIndex index.php 
RewriteEngine on 
RewriteCond $1 !^(index\.php|resources|images|css|js|robots\.txt|favicon\.ico) 
RewriteCond %{REQUEST_FILENAME} !-f 
RewriteCond %{REQUEST_FILENAME} !-d 
RewriteRule ^(.*)$ index.php?/$1 [L,QSA] 

 additional reading:
 
 http://stackoverflow.com/questions/29503934/codeigniter-showing-404-page-not-found-on-hostgator
 
 CI 3.xx
 http://www.codeigniter.com/userguide3/general/styleguide.html#file-naming