Alex Seitz-Wald has a good article on Salon on the problems with the filibuster (summary: it's probably unconstitutional, it's definitely undemocratic, and it's bad policy). But Seitz-Wald doesn't go into detail about one thing: The filibuster, and all similar departures from majority rule (with certain explicit exceptions), aren't just innovations with no justification in the Constitution; they were explicitly considered and rejected by the framers of the Constitution.
Explanation below the jump.
The thing is, the framers of the Constitution lived in a world where two countries with democratic institutions were collapsing; the Netherlands and Poland had been powerful, enlightened countries in the 17th century, but by 1795 both would be overrun by their neighbors. At least part of the blame was laid on their constitutional quirks, which were overscrupulous about checks and balances; in Poland's case, the "liberum veto" was like a filibuster on steroids.
That's why the Constitution requires supermajorities only for exceptionally grave decisions (treaties and Constitutional amendments). The fact that we now need a supermajority to conduct the ordinary business of government would have horrified them.
Just to show I'm not making this up, here's Alexander Hamilton in the Federalist Papers, the best source we have on the thinking behind the Constitution. (It's worth reading in full.)
To give the minority a negative upon the majority (which is always the case where more than a majority is requisite to a decision) is in its tendency to subject the sense of the greater number to that of the lesser number. . . .This is one of those refinements which in practice has an effect, the reverse of what is expected from it in theory.(Federalist Papers, Federalist 17, Paragraph breaks added)
The necessity of unanimity in public bodies, or of something approaching towards it, has been founded upon a supposition that it would contribute to security. But its real operation is to embarrass the administration, to destroy the energy of government, and to substitute the pleasure, caprice, or artifices of an insignificant, turbulent, or corrupt junto, to the regular deliberations of a respectable majority.
In those emergencies of a nation, in which the goodness or badness, the weakness or strength of its government, is of the greatest importance, there is commonly a necessity for action. The public business must in some way or other go forward. If a pertinacious minority can controul the opinion of a majority respecting the best mode of conducting it; the majority in order that something may be done, must conform to the views of the minority; and thus the sense of the smaller number will over-rule that of the greater, and give a tone to the national proceedings. Hence tedious delays—continual negotiations and intrigue—contemptible compromises of the public good.
And yet in such a system, it is even happy when such compromises can take place: For upon some occasions, things will not admit of accommodation: and then the measures of government must be injuriously suspended or fatally defeated. It is often, by the impracticability of obtaining the concurrence of the necessary number of votes, kept in a state of inaction. Its situation must always savour of weakness—sometimes border upon anarchy.
"Pertinacious minority." "Corrupt junto." "Tedious delays—continual negotiations and intrigue—contemptible compromises of the public good." Hamilton could have been writing about today.