The refs are indirecty controlled by the clubs, it's in their best interests to overly protect the players.
PGMOL (Professional Game Match Officials Limited, the company responsible for the National List and Select Group officials) is allegedly an independent organisation, but it's controlled by the chief executives of the Premier League, the Football League, and The FA, who constitute its board (Keith Hackett is the general manager and ultimately has to answer to them). Given that these bodies can be relied upon to do what the clubs want, it follows that the clubs can exert an influence over the officials via Hackett and frankly would be stupid not to with things working how they do.