There’s no reason to treat the US as a federation of states anymore, at least at the federal level. They’re not independent entities and haven’t been for a long time. There are certainly more differences in needs and beliefs within California than between North and South Dakota. That doesn’t mean states need to be abolished, just that they don’t have an independent nature in the federal government that justifies them having an equal say when deciding country-wide matters.

Nothing “makes sense” about giving each state equal representation, no more than expecting that state legislatures should be made up from two representatives from each town. Barely any other democracies work like this and there’s nothing unique to the US that demands a different system, it’s just the first and has some sacrifices for expediency that should have been ironed out long ago, except the people that the bug empowers value their power over democratic ideals and that power enables them to maintain it.

There’s other reasons for bicameral legislatures than giving unequal entities equal power, most of which are seen in the differences between the Senate and the House already. Senators are elected by larger constituencies, meaning they’re balancing issues from must larger areas and usually less extreme, they have longer terms giving them some resistance to quick changes in political opinion, and the split means certain tasks can be assigned to the different bodies based on whether it should be quickly reactive to changes or not.