What are repositories?
Repositories (also called sources) host packages. You can think of Cydia a bit like a web browser: consider that Safari doesn't contain or own Google or Amazon, but instead is a way to view Google, Amazon, and any other website. Cydia is a way to browse and view software hosted by independent repositories, and the Cydia Store is a purchasing system that lets you buy software hosted by them.
Cydia automatically includes a few sources, but only Cydia/Telesphoreo is run by the people who make Cydia. The sources BigBoss, ModMyi, and ZodTTD/MacCiti are independently-owned and work closely with Cydia.
Cydia is an open platform built to help you have control over your device; you can choose to add extra repositories run by other people and install any package you want, from good to bad.