Joomla! is a content management system. Sections and categories allow you to organize your content.
The basic structure is: Sections include Categories. Categories include content items (1.0)/articles (1.5).
Category A1 content items/articles Category A2 content items/articles Category A3 content items/articles
Category B1 content items Category B2 content items Category B3 content items
Category C1 content items Category C2 content items Category C3 content items
The content items/articles are what you would think of as web pages in a traditional html site.
Both section and category "pages" can be created to serve (more or less) as the home pages for the categories and sections, respectively.
Although it makes sense to organize your work into categories and sections, you do not need to show these to your users. Using your menus, you can link directly to sections, categories and content items. You can also select numerous options for the display of content associated with each type of link.