The concept of states as semi-sovereign, their established boundaries, and the principle that they are entitled to at least part of their representation on an equal basis are historical accidents; but changing that would require a Constitutional Convention that completely replaced our current system. That would more or less be a third American revolution (the Civil War being the second), and who knows what the result would be. Are we really so homogenous a nation today that regional interests should no longer be a factor?
Similarly, in a winner-take-all voting system like we currently have do we really want major national issues decided by a 50.01% majority across the entire nation?