The Senate was never meant to be proportionate, and that would be perfectly fine if the House was actually proportionate.
Edit: I'm not going to respond individually to the same point(s)... The US is a federation of states. Whether you like it or not, the country was set up this way on purpose. And believe it or not, there was a lot of thought put into it.
There would be zero point to having a bicameral congress where both houses were proportional representation. Why not just have one at that point?
Each state has its own legislative, executive, and judicial branches. They are each microcosms of a nation within the nation. The Governor is akin to the President. State legislatures are the same concept as federal legislatures, and state judiciary is analogous to the federal judiciary. But each state has some leeway in the actual specific ins and outs of how those positions operate. And it can vary slightly state by state. This has its pros and cons, but it was completely intentional.
It makes perfect sense to have a congressional house made up of representatives from each of those states to represent their state's interests in the federal legislature. The interests of a state as a whole do not always align 100% with the will of the people. People are stupid, and often wrong.
Does that make sense? It is one thing if you are advocating to eliminate the concept of states entirely. But as long as we have the federated system that we do, it makes complete sense to have a legislative body made up of two representatives from each of those states.