It's not rule by the minority. It's that the majority needs to get wider agreement on their changes if they are to be implemented. The minority cannot force anything to happen. They can only prevent sweeping changes from passing with the slimmest of margins.
For every liberal complaining about the filibuster or Senate debate rules, would you have been fine with total Republican control of all levels of Federal government from 2016-2018? They had a wider majority in both the House and the Senate than the Democrats do right now.
Slowing the pace of massive change is a good thing. It gives time for ideas to be fleshed out. It gives time for ideas to be experimented with at a smaller scale. It gives time for people to see the results or consequences of actions.
Yes the systematic unequal representation in (in descending order of inherent distortion, though abuse of state-level control of apportionment in the latter case means it's not always descending order of actual distortion) the Senate, Electoral College, and House all favor essentially the same geopgraphy and thus the same political faction so long as ideology isn't geographically homogeneous. This favors stable minority rule.