Every aspect of SharePoint is highly customizable from the page layouts to the individual controls on the page. Customization of controls allows better functionality according to the needs of the users and enhances the user experience when using the site.
Functionality on SharePoint can be customized using the .NET framework. For example, the left navigation bar will only present links that a user is authorized to use, this is controlled by the security settings within SharePoint, but this requires management of these rules for each individual that could get involved. Instead, customization of the navigation bar using the .NET framework can allow implementation of complex logic which will provide access to links based on the results of this logic.