To be sure, as with federalism, in practice the use of the filibuster for a long time was closely intertwined with the fight to preserve white supremacy. The filibusters against civil rights were never democratically legitimate because they were based on elections, especially in the South, that were themselves fundamentally undemocratic. Still, the basic idea of giving intense minorities some institutional support makes some sense.
There’s also a case for the filibuster in that it empowers individual senators; without it, especially during this era of polarization, the result is apt to be top-down rule by the majority party. That’s what happened in the House after procedures and customs that empowered a wide array of members disappeared. Top-down rule robs Congress of one of its real strengths — the ability of individual members of both chambers, but especially senators, to be influential. So as long as the filibuster is used sparingly, it can be perfectly democratic.