Earlier than that. Economic reasons were pretty big. Some small states based their entire economy on X, and if you legislated something related to X, they could get screwed big-time. And economy != slavery most of the time, guys. (People who treat the entire history of American civil discourse as though it was ONE SINGLE ISSUE for over two hundred years kind of piss me off.)
Also, religion...some states are dominated by one religion, and religious freedom is important. If they have a way of life that says Y is important, then the other states shouldn't be able to take away or change Y. It gives Utah a voice, for example. We may not agree with their voice, and we may outvote them, but their state still gets an equal voice to stand up and say "guys? can you not put contraception in that national health care system?". They get this voice because we treasure differences between lifestyles in this country, as much as we might not agree with them. In the Senate, it's not their people that have a voice, but the state itself, its history and its culture.
Iowa "deserves" exactly the same vote in the Senate that California does.
They both have suffrage, period. STATES have suffrage just like PEOPLE have suffrage. You keep bringing individual people into the equation when headcount is not what the Senate is about!