Permissions Denied

[Shibby-Shabs]

I have Cpanel Hosting and I Password protected a directory (eg. .htaccess and .htpasswd) but now it stopped working which is a easy fix but I don't really want to use it, I tried deleting .htaccess from the password protected folder but it kept saying:

Permissions Denied

I tried moving everything to a different folder but again:

Permissions Denied

I also have this in my root directory but I don't know what it is and this may being doing something.

 IndexIgnore .htaccess */.??* *~ *# */HEADER* */README* */_vti*

<Limit GET POST>
order deny,allow
deny from all
allow from all
</Limit>
<Limit PUT DELETE>
order deny,allow
deny from all
</Limit>
AuthName zippedfiles.co.cc

EDIT: I have tried changing files and deleting in the following:
Cpanel
FileZilla
net2ftp.com

Help?