I think this is because you’ve committed your ‘public’ directory (i.e. the final output) rather than the ‘source’ that Netlify will use to build and deploy your site.
If you want to build your site on your own machine, you can just drag and drop the public folder, and netlify will serve it. This is a pretty simple way to do things.
If you want to use Netlify’s continuous deployment, commit your whole project: i.e. the content, themes, static folders, without the public folder.