Virginia threw its support behind this plan because it was the best possible constitutional plan available. Madison was pushing for a stronger National government at the time but being blocked, and as a part of that national government, he was advocating the Senate have the ability to essentially veto state laws - remember that there was no Judicial Review in the system at the time.

So for the Senate to have that power, they needed to have equal representation from each state otherwise populous states would have too much influence on the internal government of other states.

That's part of it, anyway. It's more complicated and I'd recommend you read Madison's notes on the Constitutional Convention if you're really curious.