The article indicates that the incident took place while boarding, which means the door was still open. If that was the case, this was a major overreaction by the flight crew that certainly would not have happened if it had just been a guy chatting on a cell phone. No, it wouldn't be antisemitism. More somebody overreacting because they saw a guy praying on a plane.
As we all know, however, the media can leave out details that it considers unimportant but actually are relevant. My guess is that they had finished boarding, shut the door and were ready to go, but the gentleman was not done praying.
And since I wasn't there, I will gladly state that this is all pure speculation on my part.
Mike