IMO, I'm responsible to not only give the tzedaka, but to ensure it's not being stolen (or misused), b/c the money belongs to ani'em. Since the money is kadosh, you need to treat it in such a manner. And just like donations to the beis hamikdash had to be used in a proper fashion, tzedaka funds need to be treated similarly. Obviously, I can't stalk them to see what they'll do with it, but I can try doing due diligence.
In Israel, I'll find their financial statements to see what kind of overhead they report, and to see where the money is being used.
If I were in the US, and knew the driver was collecting an obscene % for driving the guy around, and that there's additional overhead for the flight/hotel/food, etc, I'd be less likely to give b/c much of it isn't reaching it's intended destination.
And if I'm in a shul, and a young strapping guy comes collecting for his family, and is followed by an 80 year old hunched over man, my sympathies lie w/ the older man, even if both of them may be mis-representing their situation.
But larger donations go to places that I can verify (to the best of my abilities).