It's not the most virulent 1%, it's 1% which have unusual mutations that cause them to be resistant to this treatment, but which usually reduce their fitness in other respects. (This can be seen in humans as well, e.g. malaria resistance->sickle-cell). The fastest-multiplying viruses are also (obviously) going to be the most common, in the absence of treatment.
This is really fascinating how being really good at something often correlates with being less good at other things (in this case antibiotic resistance seems to be inversely proportional to the potency of the bacteria).
This is true not just for bacteria but also for other living creatures; for example animals that have lots of children have very short average lifespans.
It makes me think that every living species must be at the absolute cutting edge of its capabilities genetically-speaking.
Natural selection tends to work on traits that are relevant till the ability to reproduce ends. If the trait can dominate by rapid reproduction, life span does not matter and robustness is not selected for. Generally it is not an inherent trade-off between certain traits, apart from energy consumption.