You purchased goods from Amazon - and they promised to send some portion of their profit to some organization of your choosing.

It's firmly Amazon's money at that point. You bought something from them... their choice on how to spend it. They were generous enough to have this program at all, really.

I would recommend finding a decent charity organization that speaks to you and what is important to you - and donate directly. Use services like Charity Navigator (or similar) to find reputable ones that maximize your impact.

I already do that. It was nice to see a portion of money that I'd be spending on other things also going to charity. Now I've got less reason to give that money to Amazon instead of another retailer.