First of all, most fish will not hybridise if they have mates of their own species available, so the appearance of hybrid fry indicates that the fish are not being kept in appropriate numbers and/or conditions.
Secondly, and most importantly, many of our tropical fish are relatively vulnerable in the wild (even common things, like cherry barbs). If anything happened to those wild populations, from pollution or drought, they could easily go extinct and only serious hobbyists would have and be breeding them. This was a very real risk for some fish; celestial pearl danios, for instance, until another wild source was discovered. If many hybrids are allowed into the hobby, there is a very real possibility those species could be lost altogether.
This is already happening with many species; Endlers (John Endler himself told me, when I met him at a talk a few years ago, that none of the Endlers in the aquarium trade are pure; they're all now Endler/guppy hybrids), Rift Valley cichlids and synodontis catfish.
There are, literally, thousands of fish species out there to choose from. Producing hybrids is unnecessary and damaging.
