For anyone even more skeptical of where your money goes when you donate to a nonprofit, there are plenty of resources out there for researching this. CharityNavigator is a popular one, but I donate primarily to GiveWell: https://www.givewell.org
It's a start, but it's woefully inadequate. Just take the ARRL, which is supposed to be a nonprofit organization for ham radio. They waste money on lobbyists working on absolutely pointless endeavors, and achieve nothing. But don't worry, all of the executives are well paid.
I worked with a large number of these so called "legitimate" charities and after what I saw I will never give a penny to any non-profit. You will have far, far more impact figuring out something you care about and directly spending $100 to accomplish that than giving $5000 to any of these organizations.
In what respect did you work with them? What is your main complaint? As far as I know, top GiveWell charities give malaria nets and stuff and it saves lives at fairly efficient rates.
Burkina Faso was one of Bill Gates biggest donation spots and it's had an endless series of unstable leaderships, insurgencies and coups in the last decade. This scares away both foreign investment and foreign aid. Countries like that have made lots of economic progress but seem to be stuck in this endless cycle of instability which is the bigger issue if the solution is to develop proper industry and proper modern housing sealed from insects.
Just because Bill Gates didn't solve all issues in Burkina Faso doesn't mean the donations were meaningless. Burkina Faso's GDP per capita has quadrupled since Bill Gates started donating, in addition to a lot of lifestyle indicators like child health and child mortality and so on. You certainly can't say his intervention made things worse.
This is getting downvoted, but it's a salient point nowadays.
Who watches the watchers?
Because if it's no one, then all we're doing is vouching for what could easily be scams set up by who knows who to steer our money to dubious organizations for who knows what purpose.
We shouldn't trust the watchers any more than we should trust, say, Feed the Children. Or Medecins Sans Frontiers. All these organizations should be watched in a comprehensive fashion.