The site’s navigation structure is designed separately by editing menus, views, and blocks.
You will find the same kind of separation in web pages that adhere to W3C standards. THe HTML/XHTML provides the structure of the information you see on the page and the CSS sorts out the look and feel.
With a Drupal website, the nodes hold all of the information attached to a blog post e.g. title, author, date, title. The same can be said of a news item e.g. title, content, go-live date, take-down date. Or any other content type. The menu system, as well as taxonomy (tagging of content) and views, create the information architecture.
The theme system, along with display modules like Panels, controls how all this looks to site visitors.
As the layers are separate, you can provide a completely different navigation and presentation of your content to different users or user groups based on their specific needs and roles.
Pages can be grouped differently, prioritized in a different order, and functions and content can be shown or hidden as needed.
To put it simply, at its most basic, a node is a set of related information. When a new piece of content is created, it is not only the body text that is being defined, but also its title, content, author link, creation date, taxonomy (tags), etc.