I understand the complaints by some about 3D, because it does task the eyes. And the glasses also strain people unaccustomed to the weight. So if some viewers complain of headache, this is entirely believable.
But I must admit I don't understand the complaints about the 48 fps. The old silent film era movies often seemed speeded up and jerky. But that's because the modern frame rate was faster than the rate those movies were photographed. The only way to make the 48 fps movie seem similarly speeded up and jerky is to play the 48 fps movie at an even higher rate.
When both the old silent movies and The Hobbit are played at the same rate they were filmed at, the motion is natural and smooth.
So complaints about the 48 fps seem to be complaining that a clearer image during motion is less realistic, or even unpleasant. This is hard to understand. People's preconceptions have an incredible ability to modify their perceptions. But this seems like a really powerful example.