Problem with Password Protecting Directory

Hello guys. I had my wp-admin folder password protected using .htaccess. Today I opened the homepage and it showed the password entry dialog there. It never showed here before. I checked the .htaccess in public_html folder and there was nothing related to password protection there. I commented the code in .htaccess inside wp-admin folder and password protection was removed both on home page and wp-admin folder. I don’t know how it started happening right now. Has someone hacked it? One thing more, it just shows the dialog to enter the password, whether I cancel it or enters the password, it still loads the whole page.

Any help would be greatly appreciated.