I think you are confusing authentication with authorization (and license assignment).
A login dilaog appears whenever the resource you are trying to use (e.g. the AccessPoint web page) requires you to identify yourself. Once you have been identified and authorized to visit the AP web page (done mostly through AD), the AP landing page will be presented to you. If you go any further (e.g. by clicking a document thumbnail) QlikView authorization will become active (license check, document permissions) but access to the AP landing page itself is governed as an AD resource.
If you want the AccessPoint page to be unavailable to some users, either remove them from the AD permissions for that particular server, or switch to another Authentication mechanism.