The set up you have is requesting windows authentication before authorizing users to access content. The user directory and the user directory connector is not an authentication mechanism for Qlik Sense, rather, it is a way to extract user and attribute information for authorization purposes to your streams and apps among other capabilities.
Is your user information coming from an active directory? By default, Qlik Sense accepts active directory authentication. If you are using an alternative authentication or identity management solution, you will want to investigate using web tickets or http header injection to accept user credentials (user name only) to Qlik Sense.
How do you want users to authenticate in order to authorize access to Qlik Sense?
Thank you very much for the response. I see now about the connection to the Hub trying to use Active Directory to log in. To answer your question, what I would like is for a user to hit my Qlik Hub via website, then be asked to log in(Username/Password) to keep security tight. Then once the user is logged in they would have access to view whatever streams/apps I have set them to be able to see. So from my understanding of what you said, the only way for me to do this would be to enter my users(and their passwords) into the servers AD, so when they hit the Hub they can put in their credentials to log in? Is it possible to do this with users being entered through an excel User Directory Connector for example? Such as setting a custom attribute of Password to be imported in with the users.
What I'm saying is AD is an option, or another identity management or authentication layer set up in front of Qlik Sense like you are suggesting. Have the user get to a landing page, log in there, pass the user to Qlik requesting a ticket, then redirect to the content. A custom attribute could be added to your excel udc, but it's not something you could pass through an authentication page and have Qlik Sense validate it. The user and the user directory is the validation.
If you go to Branch, there are a number of examples on how to send user info to Qlik Sense for authorization. http://branch.qlik.com/projects/forumdisplay.php?31-Security-Integration
Check out the access control test module.
In addition, have a look at virtual proxies which allow you to set up entry points for multiple different auth schemes.