Actually I have seen many posts around the internet that say the pilot is in charge of aircraft so pilot is responsible. Many think the man could not have been forcibly removed without pilot order. Pilots used to have complete control of aircraft, no matter what. I think after all the changes after 9/11 that is not so true any more. When in the air I am sure pilots still are in charge but on the ground I am not sure they are.
Pilots are ultimately in charge but I doubt the pilots get involved during the boarding process unless needed. No one to this point has claimed it was an order by the pilots to have the passenger removed. We shall see.