The system wasn’t built to favor rural areas, it was built to favor the sovereignty of the States, which are independent territories with their own systems of government, who specifically agreed to join the US in exchange for the representation they received in Congress and the Electoral process. Trying to walk back that compromise to let high population states dominate national politics is a violation of the social contract.

That’s why the States are referred to as experiments in democracy. It’s a decentralized form of government (With guardrails, written into the US Constitution). It doesn’t matter that there are millions of people in Los Angeles, their voice shouldn’t have a disproportionate say in how farmers in say, Iowa, run their government. The needs, economies, and demographics of different states are completely different and a using decentralized system of government is much more intuitive than trying to manage it from the top down.