Because the United States was designed with the basic understanding that *how many* people is important, but it's also important to prevent population centers from controlling everything. The idea is to prevent tyranny of the majority as well as the minority.
Just think about it; if you, like me, lived in Montana and we had either one chamber of Congress or two as now, but both split by population, then we in Montana effectively have no say in the decisions of the nation. My state and its few residents would be wholly inferior, second-class citizens essentially, to the likes of Texas, California, New York, Florida, etc.
Yet those states rely on Montana for a LOT of things. We are a massive exporter of meat and grain products to the country and world. We ship trainloads of coal to the West Coast daily (they often make me late for work) and ship cattle and Boeing aircraft components across the nation. We generate billions in tourism revenue because of our massive wilderness areas (great for hunting, fishing, and generally recreating). Our mines literally built the world (read about Butte Mine). Yet our largest city doesn't even have a million people in it.
None of these industries lend themselves to large populations, yet Montana as a state is a thriving and vital part of the United States. Why shouldn't we be given equal representation in part of the government? What makes New York as a state more important than Montana?
That is why we have one chamber for population and one for states. The Senate is supposed to be the throttle that ensures population centers don't pass policy that needlessly disenfranchises smaller states. The House though entirely allows for that because population needs to be taken into account as well. Were the system entirely based on state equality, that would be equally unfair to large states like Texas and California.
Does that help? I feel it was pretty good...