This is a very nice incentive from Apple. That said, I'm wondering if they have considered the possibilities for a PR disaster when employees give to the not-so-admirable organisations, and Apple have to do the same. I mean, not everyone fight against hunger, aids and the like. Some are politically controversial, some are crazy while some just promote hate. These can still be non-profit.)
Yes they can be non-profit but can they be 501c3.
In order to be a 501c3 your organization can spend only a very limited part of it's budget on political issues. Most of the money must go to some service. The IRS has some rules on this
A big organization like Apple will not have to worry because the views of their employees roughly match those of everyone else. So on whole Apple's giving will roughly match the public's opinion of what's best.