If you don't wish to get into the technicalities, then consider the
big picture: if a monopoly is not violating individual rights, i.e.,
not initiating aggression against a non-aggressor, then it is
perfectly justified by libertarian theory, no matter how much of the
market it captures, no matter how many "little guys" do not have the
resources to compete against it, no matter how high its prices and low
its quality.
I see what you are saying that the basics of Libertarian theories rests on the individual, especially in terms of aggression to one another. However, as I see it, there's also the importance of individual freedom, or the right as individuals to choose. If there is a monopoly, there's not much of a selection, either we buy it or we don't. However, what if my happiness rests on having a material object (such as oil, which is important to me, because I like to drive from place to place or maybe it is important to my job), but what if I want the best product either in terms of quality or price or both. With a monopoly, I can't choose that; because oil is so important to me, I will pay whatever it takes at the pump. Monopoly also brews inefficiencies, just look at our state's welfare projects, that's one of the many reasons why we think privatization is necessary. We all know, or at least should know, that a free market, one in which competition is ripe, would ensure our individual freedoms. Therefore, a monopoly threatens market competition, therefore a free market, therefore our consumer well-being, therefore our individual freedom.