Renovate will silently ignore any repositories that don't have a `package.json` file, however most people choose to select which repositories to include. Unfortunately GitHub doesn't yet offer the chance to "select all but exclude some" so instead you need to select all that you want. The form also requires you to start typing before it suggests to you repositories, which is a bit of a pain.
Once you're done selecting repositories for Renovate to run on, click the green Install button at the bottom of the page and Renovate will be enabled for those repositories and start the onboarding process.