Most of the pathogens found in aquaria can co-exist in harmony with fish, it's typically only under stressful conditions, when a fishes immune system becomes compromised when the parasite/pathogen gains the upper hand.
Having said that, I think that a very important factor has been missed by many hobbyists, that being selective breeding. In today's designer fish world, many strains of tropical fish are bred for qualities other than disease resistance and some of these strains may be more susceptible to disease by their actual genetic make up. IMO flowerhorn often fall into that category.
How many breeders of flowerhorn focus on disease resistance when attempting to wow the world with their latest greatest new strain of fish? The same could be said for Discus, Angel fish, and many other species that are in demand, where the latest new colors, patterns, fin length, kok size, etc. are what is driving the market. Realistically, disease resistance is most likely at the bottom of some breeders priority list, if it's even considered at all. Nature has it's own way of taking care of genetically weak specimens, many breeders will take those same fish & breed them for profit.
IMO the key is starting out with a healthy specimen with a strong immune system, followed by keeping the fish in a low stress environment (which includes clean water) and fed a premium diet. Remove any one of those factors from the equation and you can eventually have problems. This is exactly why even when kept under the best of conditions, some fish still succumb to disease. (weak immune system, and low resistance to disease) With these fish one could simply miss a single weekly water change, and it would be enough to upset the natural balance within their system. Yet other fish with stronger immune systems, and greater resistance to disease, can live in what many might consider horrendous conditions, and seemingly thrive.
Last but not least, from what I have seen, and read, many FH keepers feed diets that IMO are less than ideal for the fish (high protein/high fat) and overfeed by massive amounts in order to "pump the fish up". This is another sure fire way to fung up a perfectly healthy fish. IMO instead of "pump the fish up bro", the mantra should be "patience bro". If the genetics are there, and the fish is properly taken care of, it will show its full potential soon enough.
