There are two kinds of torrent sites: public and private. Private torrent sites require you to be a member of the site, and only then are you able to download any content. Private sites also may have a whole bunch of seeding, downloading, uploading rules in action. So you cannot just download something and remove that from your client after download is complete. Such sites often require interviews or invitations from existing members.
Now in Jackett, you can add both public torrent trackers and private torrent trackers (if you are a part of them). Each site may provide their own API key or sometimes just username/password, or sometimes nothing for public trackers.
Edit: It could also include usenet indexers.
TL;DR: Indexers are torrent sites (public and private) that you add to your jackett with either API keys or username/password or nothing in cases of public sites.