Then you've probably not been using it right.
Salt is much safer that many of the common whitespot medications that contain copper and/or formalin. It's recommended by vets as a safe alternative. It's the best way to treat species like loaches and catfish that react badly to copper in particular.
The common misunderstanding is the idea that medicines are safe -- they are not. Almost by definition, they're poisons, and what makes them relatively safe to use is knowing how much to dose so that it kills the pathogen or parasite without yet killing the host (the patient).
Used at 2 gram/litre, tonic salt is extremely well tolerated by even soft water species. Raising the temperature alongside the salt speeds up the whitespot life cycle, speeding the whole thing down to a 1-2 week usage of salt. After that, do the water change, and the parasite should be eliminated from your aquarium.
Salt has little to no value when treating fungal infections. True, fungus is rare in brackish and marine aquaria, but the safe salt concentrations around the 2 g/l mark seems not to be a useful therapy for fungal infections in freshwater tanks. Methylene blue is probably the least toxic treatment, and can be used safely with even baby fish and eggs. But it is a relatively mild medication, so best used to prevent fungal infections (e.g., on injured fish) or very slight infections; if the fish is seriously "fluffy", you might find a more potent, but also more risky, medication works better.
Cheers, Neale
PS. For what it's worth, the Common Plec species is abundant in brackish water habitats in Florida; clearly, the much lower salt concentration needed to treat whitespot will have no impact on its health.
Be careful with the salt. The pleco, kullis, and rams are sensitive. Some people may get away with using it, but with plecos and rams, I've never had much luck using salt.