I think one of the points of the beginning of the article is that in terms of numbers "the countless charities doing good in the community", or as it put it later in the article "can help empower ordinary people" are, in terms of donations the exceptions. While I don't want to sound dismissive, we shouldn't be creating overall policy based around the exceptions.
And I get it as I understand the challenges of one of your major concerns in life being a disease that 30,000 out of 330,000,000 Americans have or 70,000 of 7,594,000,000 of the world population. (This is Cystic Fibrosis which killed my baby sister almost 40 years ago. I think your own concern has roughly the same kind of rarity.) And I get that the break through treatment for some about a decade ago came because the CF Foundation gave up on government and market interests aligning and invested directly into private sector research companies. So I get the "small number" exceptions and the good that charity can do and am not suggesting that we don't care. I just think that we can find a way to keep these charities getting their pennies while stopping the funding of small fortunes [by tax payers] to the latest cathedrals and power grabs of the rich. Sure we will probably make mistakes and do harm here and there as we move to a greater good, but I think we are overdue to take the journey. And I'd like to think that the need for good many of these countless charities goes away.
I pray for the day that the CFF can close its doors! I pray for the day that no one quite remembers why it was needed to begin with. I doubt I'll see it unless there is some form of awareness in an afterlife.