You have accepted that if there was an incident involving Costa, you could understand the need for increased fines/sanctions. Yet in the case of sanctions regarding the control of players, you can't accept this rationale.
This season, Chelsea had 3 previous offences for failure to control players/behaving in a disorderly way. You are not the only team to be charged with that this season, but you were the team charged most often. Go to the FA's Governance page and have a look through the reports for yourself. I have just highlighted the ones relating to Chelsea.
Whether the prior fines were fair or not the club got them.