My niece has Joubert Syndrome, a disease that has an incidence rate of roughly 1 in 100K. ALS is 2 in 100K.
One of them is fashionable, the other is not. It all seems to be about marketing. That's my only point.
Contact sports are seen to be one of the causes, so it hits home to athletes. Also, marketing is a huge part of getting donations. I've read studies that donation organizations that spend money on marketing, while a lesser percent of each donation goes to the actual thing they are advertising (some goes to advertising, obviously), the total they are able to get in donations far eclipses the total for organizations with little to no marketing budget.
Also, (I don't know a lot about it) it looks like Joubert Syndrome is from genetic mutation. ALS is and isn't. Plus, ALS isn't diagnosed in infancy. In fact, exact diagnosis is hard and usually based on symptoms. They pretty much have to test for and rule out every other disease with similar symptoms.
Take into account that and that there are a ton of diseases lacking in funding, and one has to be favored over the other. It could simply be because someone with some marketing power knew someone with it and spread the word on their own accord.