Using command line arguments with PHP requires the use of the $argv array. This is only avaialble if the register_argc_argv setting is enabled, but this is disabled by default.
To enable register_argc_argv you would need to create a php.ini file in your web space (or edit the existing one) and include this line:
register_argc_argv = On
You can then specify this php.ini file in the command for the scheduled task, for example:
/usr/bin/php5 -c /home/sites/domain.com/php.ini /home/sites/domain.com/cron.php argument1 argument2
The PHP script will then be able to use the specified arguments.