The respect code of conduct is separate from the rules of the association. The only charge they can make from public comments is improper conduct which Mourinho was charged for. It states, "manner which is improper or brings the game into disrepute or use any one, or a combination of, violent conduct, serious foul play, threatening, abusive, indecent or insulting words or behaviour". Mourinho was charged for acting improper and bringing the game into disrepute by claiming a conspiracy against his team. The FA won't charge for just criticising a referee, however they will if managers imply bias. There's a big difference between criticising a referee performance and claiming a conspiracy against your team.