I've previously added filters to JournalArticleLocalServiceImpl Class before calling addArticleResources() method and setting the addGuestPermissions boolean to false to disable default permissions for Guest/Site member roles on WEB CONTENT.
The change reflects on control pannel--> Web content, but not on WEB CONTENT DISPLAY PORTLET.
What needs to be done to disable default gues/site member permissions on Web content display
liferay version: 6.1.2
If I understand you correctly, you have an article which does not have guest view permission. When you add it to a Web Content Display Portlet, the portlet's permissions are unchanged?
In case this describes your situation: Note that this is completely expected: The portlet is configured to show any article. When the portlet is "protected", this has nothing to say for the article. A read-protected article on the other hand would leave an empty portlet, e.g. the article would not be shown, despite the portlet's permission.
If this does not describe your situation, please describe with more detail