I think the "gluten sensitivity" craze is a perfect example of this phenomenon.
I wouldn't call a disease that affects around 1% of the population "very rare".
It's true that there's a gluten-avoidance fad that has drawn in lots of people with no medical justification, so that not everyone who demands gluten-free food is necessarily a celiac sufferer. "Gluten intolerance" seems to be a fashionable ailment these days, with perhaps varying degrees of validity (and potential confusion with other issues that may have similar symptoms), but sources suggest that around 3 million Americans, for example, really do have celiac disease.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3496881/ http://www.uchospitals.edu/pdf/uch_007937.pdf
There's nothing wrong with describing a rare thing as rare.
1. It's not been clearly established that gluten sensitivity doesn't exist. Even if current medicine hasn't established it, it's actually quite common for established medicine to be slower than alternatives (e.g. probiotic, medical marijuana, babies needing touch and breast milk).
2. For gluten sensitivity, it's not clear if you're denying people have physical symptoms (bloating, gas) at all, or whether they are misattributing them to gluten. Either way, I don't see a connection.
3. Your comment really has the affect of associating two very different, very emotionally charged things that I think is lazy and exhausting to debug.