It's a combination of everything. I've heard (admittedly only anecdotally) that a well thought of ref in the lower leagues refused the 'promotion' to the Premier League because he wouldn't interpret the rules the way they wanted him to. I think it's reasonable to believe that the fouls that ref's don't give - for shirt pulling/pushing in the penalty box, those that they do give for lesser contact outside the box, is a result of the unspoken/unofficial rules given to them by the Premier League. I also suspect that they are told 'if in doubt, favour the big (money generating) teams'. This inevitably leads to unconcious bias. I alo believe that there is corruption - given the amount of money involved it would be incredibly naive to think otherwise (depite the knee-jerk denial of every one of the pundits - eg; those on the gravy train).
There's a lot of nonsense spouted about 'the ref letting the game flow' and 'keeping 11 v 11 on the pitch. That's not his job! His job is to enforce the rules.
Lasty (you'll be relieved to hear), i don't think that ref's should be laughing and joking with the players or on first name terms with them on the pitch. Rugby refs aren't. They'll call the captain over or say 'number 6 you are being penalised for....' - it lets players know (sublimally) who is in charge.