While that's correct, it doesn't alleviate any of the fears. Virus->Something transfer isn't relevant unless Anything->Virus transfer is also common (which doesn't appear to be the case?). Plant->Plant or Bacteria->Plant transfer are really the ones relevant to GMOs, and neither seem to be common. So we really can't say that genetic modification is just like what nature does, except for uncommon edge cases.
I'm no expert here but from what I've read bacteria can be used as vectors in genetic engineering. I think this is an important point to mention since GMOs are sometimes seen as playing god, while I'm not sure if they are really so different from traditional selective breeding techniques. In the end, we should evaluate these techniques based on how safe they are, rather than thinking about "naturalness".
Whilst this is recent enough knowledge to not be included in what most people here would have learned in high school, we have found many genes that have been transplanted laterally. We are technically not sure this was by viruses (perhaps it was by bacteria or even somehow directly).
Genes do spread without procreation. This is a certainty at this point.