The senate was more of a temporary system to make the colonists happy. It doesn't make the government fairer today.
It was never meant to be temporary.
trey: I'm out of my depth talking about the founders, but my instinct is that the way the government is structured has more to do with the interests of the people who created it than anything else.
Either way I don't think the Senate is a great way to protect minorities in the year 2008.
I assume you are refering to the Connecticut Compromise. In which you are right, it was a compromise between the larger states only wanting popular represenation and the smaller states wanting to have a say. Another good point is that the founding founders likely did not imagine the large population difference between states that exists today.
However on the other hand, the Senate was never meant to be a democratic branch for the popular opinion. Most of the founding fathers invisioned it as a longer term group that would ignore public opinion and try to restrain the "fury of democracy". Hence the whole "not voted by the people" aspect the Senate originally had.
While you have a good point that the Senate gives too much power to smaller states, I would say it is unwise to overlook the Senate's purpose in protecting the minority opinion (or in this case, the small state's opinion).