And this is what ffmpeg have to say about donations:

Want to donate to FFmpeg? Well, theres no way to do that currently. Luckily we dont need any money. But there are many not for profit organizations with noble goals that do. Select one of your choice that you trust and agree with their goals and instead of donating to FFmpeg, send your donation to them. http://ffmpeg.org/

So yeah, donating to VLC directly seems like a good choice.