It did make sense, but I understand why it might not seem like it to "modern Americans". In fact, it's quite an interesting mental challenge of putting yourself in someone else's shoes.
We have a similar issue today in the EU. Do we base it one "one country, one vote" or on "one person, one vote"? Both sides of the argument is valid. Why would small countries join if they give up complete independence to the giants? I imagine the situation was very similar when the US was formed.
I think the flaw in the US system is they failed to forsee that states (or rather, people) would see themselves as one country and not a collection of countries. There should have been a time limit on the discrepancy of voting power.
Sure, for a hundred years, a state is where your loyalty, your feeling of self, your center is at. But as time moves on, you are less an Ohioian and more of s USian. Similarly, I would hope, you are less of a German and more of an EUian.
Neither blocks seem to have taken this into consideration but it makes it none the less true. Future generations paying the price for previous. Yada yada....