I met a couple of refs during my courses in the UK and they talked openly about how when they did their courses they were told that not all players and managers should be treated the same. I remember the quotes "you wouldn't treat Costa and Scott Parker equally, would you?" and "there were four managers that we should treat differently from the rest: Wenger, Mourinho, Sir Alex and Rafa Benítez" (this story dates back to 2004-2007, more or less).

So yeah, there is a not-so-unconscious bias. I would argue that the English refs are the best in world, however. Whatever they do is to protect themselves, not unlike any other organisation. For instance, regarding those four managers who were to be treated "better than the rest", it was because they had political power (in the world of football, that it). So it wouldn't bode well for you if you were a ref and pissed off Sir Alex or Wenger excessively. If you stepped over the mark and got too far in, their vengeance could affect not only your job, but also that of your peers. If you pissed off Houllier, nobody would really care.