Is there any way via a cron, or a script that I can make it delete all files in x directory daily?

Add that to your crontab file replacing <mins> and <hr> with the minutes past the hour you want to action to occur. i.e. 0 5 would make the command execute at 5am every day. 0 20 would make the command execute at 8pm every day.

>/dev/null 2>&1 prevents cron from sending an email to your user mailbox each time the command is executed.

Could I make it 0 0 and make it execute at midnight? And is there a way to make it so it doesn't delete certain files, such as a .htaccess file?

Thanks a ton for your help.

Yep, that is fine.

As for not deleting certain files... the command I gave can't do that. However you can write a script in your language of choice to perform the deletion of files and then add the path to the crontab entry.

e.g. /path/to/php /path/to/delete-script.php