Yeah I'm the same. I understand there is a pressure equalization type of affect, like taking off in a plane, but you get used to that after a week or two. Maybe if people have bad sinus issues then that can cause headaches, in which case they already have serious issues and the headphones 'pressure' effect triggers pain. But that's reaching IMO.
I've been using them between 4 and 6 hours a day at work for 3 years now.
The only other thing I can think of is loudness causing a problem:
https://en.wikipedia.org/wiki/Loudness_warLoud (in terms of dynamic range) can easily cause headaches after prolonged listening even without headphones. If these people are listening to loud music at high volume with these headphones that could cause headaches easily.
In fact, compared to my other headphones I found myself lowering the volume on my QC35's quite a lot. My comfortable listening volume is now ridiculously low, you don't need it loud with the noise cancellation. So for example, on 'normal' headphones, I might listen to the music at 60/100 to 100/100, depending on the situation, with the QC35's I rarely go above 10/100, usually lower in fact. So I think these people either have sinus issues or are listening to dynamically loud music at medium to high volume, or both. The fact the author states he was getting a headache and the noise cancelling wasn't even on suggests listening to loud music at high volume, in which case you'll get a headache no matter what headphones you listen on.