Well, having worked in both the non-profit sector and in public health, I think the criticisms of the Gates Foundation's public health efforts are malarkey. It's basically an opportunity cost argument and by that standard virtually every charitable foundation is wanting. Why are you spending money on the ballet when there are kids who can't read? Why are you spending money on literacy education when there are kids who don't have enough to eat etc. The problems of the world are endlessly varied and complex, and you can't ask much more of anyone than that they pick a spot and take a whack.
That said, the idea that spending money on infectious diseases is wasteful is particularly inane. Sure, in some places obesity may result in more premature deaths than malaria, but the fact is nobody really knows how to effectively fight an "obesity epidemic", whereas malaria is clearly eradicable -- and once it's gone, it's gone forever, because P. falciparum has no natural host other than humans. The same goes for communicable diseases for which we have vaccines; we know how to fight those cost effectively, even eradicate them in many cases. The missing piece of the puzzle is money.
Now criticism of the foundation's education efforts is a lot more warranted. Just like everybody thinks they're qualified to design a website because they have opinions about which sites they like and don't like, everyone thinks they're qualified to redesign the educational system because they went to school. The difference is that Gates has the money to make his bad ideas materialize. It may be hacker philanthropy, but most attempts at "hacks" result in kluges.
So overall it's a mixed bag. While you do have to give props to Gates for being "the man in the arena", sometimes, unlike in Teddy Roosevelt's famous speech, the man in the arena's failings don't fall exclusively on himself. So while philanthropy is admirable in itself, where the philanthropist's activities impinge on areas of public policy like education his actions should be held up to scrutiny like anyone else's.