Republicans control the senate despite only having 40% of the popular vote nationally in the Senate races.
Californians pay 13% of the Federal tax revenue and get the same number of Senators as states that contribute less than 1%.
That's because the Senate is there to represent the states themselves in the federal government as individual political entities.
IMHO, if you want pure majority rule everywhere, you might as well just abolish the Senate entirely, as it would be redundant with the House.
Personally, I think some kind of geography-proportionate representation is necessary to prevent the non-urban areas from becoming neglected hinterlands. That said, I do dislike the way the Republicans have used this system to extract maximum partisan advantage, so some reform is necessary. Rather than making the Senate representation proportional by population, I think it should lose its monopoly on executive/judicial confirmations and the House should have equal say in those.