As per Codeigniter documentation, by default, the index.php file will be included in your URLs:
example.com/index.php/news/article/my_article
And you can easily change the URL and do mod_rewrite using .htaccess. See below.
RewriteEngine on
RewriteCond $1 !^(index\.php|images|robots\.txt)
RewriteRule ^(.*)$ /index.php/$1 [L]
Unfortunately, this is NOT working with GoDaddy, and to resolve this, instead having the above .htaccess, your entry should be like this.
RewriteEngine on
RewriteCond $1 !^(index\.php|images|robots\.txt)
RewriteRule ^(.*)$ index.php?$1 [L]
Hope this helps you as well.