I don't think there's much evidence that active displays give people more headaches than passive. 3D itself can give people headaches for a number of reasons such as eye muscle imbalances, or the need to focus on the plane of the screen but move your eyes as if you're looking at different distances. However, these are all temporary and headaches and eye strain tend to go away with more exposure to stereoscopic 3D as your eyes and brain get used to it.
Some people will say that they got headaches when they had an active display, but less so with their newer passive display. It might make sense at first to blame the active display, but you shouldn't forget to factor in having had more time to get used to stereoscopic 3D itself. Passive displays are relatively newer and less likely to be someone's first experience with a 3D TV. There's also more 3D content available now than when active was the only option, so people are also more frequently viewing 3D, which itself would lead to fewer headaches.
I had tons of eye strain when I got my 3DS. I've never had eye strain with my active DLP projector. But this doesn't mean glasses free displays give me eye strain, it's just that the 3DS was my first significant exposure to stereoscopic 3D.