You are probably overthinking the answer. It’s simple: it doesn’t get used because it is not yet a tool for your organization. If you SP site is a group of links to other sites, people don’t need to go there, they simply bookmark their favorites sites on their favorite browser. If your SP site is a place to store forms, but those forms have existed on your network for years and are still there, people will go to the old place to get the necessary documents.
To drive adoption, design your site to have great functionality such as the ability to fill in HR forms online and have them electronically routed to the right people when the user submits the form. Use your SP site to regularly share important as well as fun information about your organization. Implement workflows and forms and collaboration modules to make this a tool. Yet, be sure to make it cool. Don’t recreate the mess that may be in your old network storage. And be sure to continually communicate the features of the site, train the staff and implement the feedback mechanism so you will know what they want and need.