Yes, I'm happy that there has been an advance for ALS, but if you take a step back, it does appear that there may be a misattribution of limited research dollars.
Except that the Ice Bucket Challenge did not misappropriate research dollars. They created new research dollars out of thin air. There is not much reason to believe that the people who donated in response to the Ice Bucket Challenge would have otherwise donated those same dollars to some other, more common disease.
The money could have been donated to more common diseases, but probably wouldn't have. Humans are mostly motivated by emotion. The Ice Bucket Challenge captured the imagination of a ton of people and got them motivated to donate. If other common diseases need more money, they should find similar ways to pull at human's heartstrings (obviously they do as well, just not with such a public feelgood novel viral stunt like this).
The question was should we leave funding to internet campaigns, not will we. I can't imagine the OP is arguing that the ALS association shouldn't take the money or that people shouldn't donate. The OP is arguing that they shouldn't have to rely on these kinds of campaigns to solve large problems like this because we should increase public research funding.
A chance reasonably larger than zero is better than a chance very close to zero.