It's not so much a bias of rural over urban, but lower population states versus larger states. You could be urban and just be smaller in size. This part of the "great compromise" was actually for smaller, non-slave states like Delaware. Virgina, the largest state in the nation at the time and a slave state, proposed the Virgina Plan, which proposed the creation of a bicameral national legislature, or a legislature consisting of two houses, in which the “rights of suffrage” in both houses would be proportional to the size of the state. Small states objected, because they'd had equal representation under the articles of confederation.

https://www.senate.gov/about/origins-foundations/senate-and-...

The overall final compromise did include compromises to slave owning states, but this vestigial is not due to those compromises. In fact, they were against it.