While I like LPH' idea, I also would be more bold myself. My mom, in fact, did the same thing a few years ago - donated a lot of money in "my" name to help build a new building for her church. I flat out told her that I didn't go to her church, and that my beliefs were a little different and that I wouldn't mind if she donated to X, Y, or Z, but I was not happy with her choice.
Since then, she's bought me gifts instead. Honestly, the donation idea was fine with me, just not which donation.
I used to receive $20 ornaments from my step grandmother that she purchased from a nature conservancy local to her where x% went to them - I thought that was great. The combo of the little token that I go, and the smaller dollar amount made it alright that it was their choice. It also wasn't a religion (which I don't believe in giving to unless its mine for me!).