We have two hosting packages at godaddy. Our live website is working fine using following .htaccess file. Website is accessible without using index.php in url.
in index.php you echo "test" and run .then you can check whether it is called or not.
in config file enable error log .
Make your /application/logs folder writable.
In /application/config/config.php set. $config['log_threshold'] = 4;