I was pretty disappointed to see that, especially at a crucial time for electronic freedom with SOPA and PROTECT-IP looming. I'm sure the boosts from HIB were helpful to EFF, and if anyone needs a boost right now, it's EFF.
Supposedly the HIB people voted, and the Red Cross came out slightly ahead. I'm kinda bummed. I might go donate a couple dollars to the EFF anyway.
They also said that the EFF would be returning as a charity in future bundles.
50% to EFF has always been a reason to buy humble bundles for me. With SOPA I'd have probably paid more this time. I half expect EFF to be added back in, so I'll be waiting on this bundle.
If that's stopping you, you can still donate directly to EFF.