Manchester United chief executive David Gill believes the Football Association singled out the club for "harsh" punishments last season.
Striker Wayne Rooney was banned for two matches for swearing into a TV camera.
Boss Sir Alex Ferguson was also handed a five-game touchline ban for comments made about referee Martin Atkinson.
"There were some poor-ish decisions that wouldn't have necessarily hit others - the actual punishments were harsh," said FA board member Gill.
"That's not to say I'm condoning Wayne's comments, because I don't think they were correct, or what Sir Alex said, because it wasn't helpful.
"We're possibly being caught up in being one of the biggest clubs and the [FA's] Respect agenda being there.
"What better way to demonstrate the authorities are being tough than by hitting one of the biggest clubs the hardest?"
Rooney admitted to losing control in the league match against West Ham in April, while his manager Ferguson received his touchline ban for comments made about Atkinson's performance during the 2-1 defeat by Chelsea in March.
Ferguson received a three-game ban for the remarks and saw a two-game suspended ban he had previously earned for saying referee Alan Wiley was not "fit enough" to keep up with play activated.
Gill, who was quoted in a new book about United called Champ19ns, questioned whether other players who commit a similar act to Rooney will receive the same punishment.
"The club doesn't condone it but Wayne recognised it was wrong and apologised almost immediately," said Gill.
"We have various issues with the ban - one being consistency. What's going to happen now? Is the referee under pressure to send everyone off?
"It's a dangerous course the FA has gone down, because consistent application is what's required and I'm not sure that will necessarily happen.
"There are certain things you should wait until the start of the season to change."
Gill was elected to the FA board in 2006 when he replaced former Arsenal vice-chairman David Dein.