Sometimes in your catalog structure it may be necessary to have categories that are for structural and/or organizational purposes only. You would use these simply to categorize your other categories and they wouldn't typically have products in them.
If you want these root categories to show products however when customers are navigating your site it is very simple.
First a before photo. This is a category grouping all Offroad products together. It doesn't actually have any products directly in it.
To get this category to show products from it's subcategories we'll go to Catalog > Categories
Then Navigate through to find the category you want to modify. Click the Edit icon
Then in the Category Editor, check Yes for the setting "Show Products for Sub Categories"
Voila! Now your root categories don't appear empty.