One big advantage viruses have in terms of being a mechanism for variation is that they can replicate themselves and cause the same variation to occur in many i

One big advantage viruses have in terms of being a mechanism for variation is that they can replicate themselves and cause the same variation to occur in many individuals within a population. If that variation causes those individuals to be unable or unwilling to mate with the uninfected, those individuals can still mate with each other. Specific mutations are vastly less likely to be present in even two individuals within a given population. So, even if most of the modifications that viruses make are deleterious, as you say, if a virus comes along that confers some advantage, it is much more likely that the resulting change will be in play in the descendants. A beneficial mutation on the other hand would have to somehow be happening in some sort of Genghis Khan creature with scores of offspring to have the same reach as a beneficial virus. So you can see the probable relative importance of these two bases of variation.