Don't know, everybody seems to bash 3D these days. When I watched Avatar I thought it was pretty awesome and didn't get any headaches either. Maybe it's no good having a 3D TV at home and expose ourselves constantly to fake 3D every day, but watching a movie every now and then in the cinema can't be that bad.
Edit: Also, all these people are just speculating, there's no science backing up any pro or anti 3D claims. I would be careful giving Nintendo 3DS's to small children, that are still developing vision, but as I said I don't think watching a 3D movie every now and then is a bad thing if you enjoy doing so.