Looking back, from a systems perspective (not necessarily the view taken at the time), the Senate was created to represent the structure of government. They were supposed to be the old party hacks from each state that were sent to DC to help architect and fix the architecture of the federal government. Their interest was in the system, in the political structure and operation of the government, not making the folks back home happy with their votes. They were more like judges. Our own little homegrown aristocracy.

Looked at it that way, it makes sense that each state should have an equal number of representatives. After all, the federal system was supposedly created and maintained by the states. But after the Civil War flipped that around, and the 17th amendment called for the direct election of senators, they were really mis-configured for the job. As many people point out, now they're just direct representatives of the people, only with a mission created from the old ways of doing things. So why are they elected like this again?

As you say, we're stuck with it now. The only way to answer the criticism of giving states equal senators is to use an argument that is no longer valid. [Insert long discussion here about how nobody wanted a democracy in the U.S. It was never a goal and it was feared by the founders]