I give to the top charities on GiveWell [1] instead. As an individual you can't help everyone, at least with GiveWell you can be fairly sure your money is making someone's life better.
If you mean "how can you know you can trust the charities on GiveWell", the whole point of GiveWell is to rank charities by how effectively they use their donations to help people.
If you mean "how do you know you can trust GiveWell", I guess you don't.
The point of GiveWell is that they thoroughly investigate the results of the charity, and recommend places that are highly effective for your marginal dollar.
Maybe they don't succeed in their mission, and they are the first to point out their limitations.
[1] http://www.givewell.org/