Setting up cron jobs on cPanel
if your user has cron access, you can always create a file, call it cron for simplicity sake, in the file add the command you wish to run, for example mine is a bit interesting cause I have to export my civicrm settings at the same time:

export CIVICRM_SETTINGS="/home/domain/public_html/administrator/components/com_civicrm/civicrm.settings.php"    
cv api --user=cron job.execute


mind you, thats using the CV command, however, this can still be implemented via the cli.php.
Example:

 /path/to/php /path/to/civcrm/bin/cli.php \
  -s example.org \
  -u myusername \
  -p mypassword \
  -e Job \
  -a execute


save that in the file you created earlier (with your changes of course), then with cpanels cron, just  set the command/job to execute:

sh cron &gt; /dev/null


or 

sh cron &gt; /home/domain/logs/cron.log


just make sure the file is outside of the web folder and is executable.