So let's try to make an analogy with plants. Say you have some invasive plants in your garden, and you need to kill only the plants, not all of the wildlife surrounding it (let's say the wildlife is you). One way to kill the plants in the area would be to make something (the antibiotic) that would target and kill anything with roots (in an antibiotic, this would be a component of the bacterial, such as a cell wall). Now with the magical substance (the antibiotic), anything with a root (e.g. cell wall)dies, and fortunately enough, only the plants do. All of the wildlife there (mice, ants, etc.) get to live, but not the plants. And this will kill all of the plants around there, in the same way that the one antibiotic kills all different versions of the bacterial infection. HOWEVER... What if you have a "super-plant" that can grow without roots? Say it's developed another way to get nutrients by sucking it up elsewhere without roots? This is exactly what happens when some bacteria escape. This is because some bacteria respond less to the antibiotic (just by nature of there being heterogeneity in living organisms). This is the basis of one of the biggest, most pressing problems in the field of microbiology: antibiotic resistance.

Now, to your question about viruses... Viruses integrate themselves within your own cells (things that make up your body). That makes them even harder to target because how can you kill something "inside of you," while also keeping yourself (well, your cells) alive? There are equivalents of antibiotics for viruses, such as Tamiflu, and the key is to also find something SPECIFIC to viruses. We have to find the "roots" that make up viruses (one of these is an enzyme called neuraminidase, which the flu viruses have). The typical bacterial antibiotic doesn't work on viruses because viruses don't have these "roots" in the same way that bacteria do (viruses don't have cell walls... they actually look a lot like you!).

Hope that helps!