enter in a subdirectory of my FTP

I have problem entered in a my subdirectory where i have installed a CGI script…this is the directory

https://www.mysite.com/cgi-bin/script/admin/admin.cgi

there is htaccess protection in this directory, but the problem is this:

when i click on https://www.mysite.com/cgi-bin/script/admin/admin.cgi to enter in the panel admin i’m redirected in the homepage. If i delete the main .htaccess created by WordPress i can enter in the panel admin.

what is the problem ?