The 1-0 loss left Derby eight points from safety as Rooney was unhappy with the refereeing in Wales.
Uche Ikpeazu struck the 85th-minute winner, with Rooney insisting that Rams forward Festy Ebosele had been fouled before Cardiff launched their decisive attack.
"Referee decisions I felt all game were not good enough. Fourth official - a lack of respect in how he speaks to you," said Rooney.
"No-one wants us in the Championship next season. That's been clear all season. We've had our punishment, but ultimately, I think, the real punishment is going to League One.
"We've exceeded a lot of people's expectations and it's caused issues."
He continued: "I need to ask questions because they deserve a bit more protection than they are getting.
"Football's a cruel game. We had complete control and the future for this club on the pitch is bright if we can keep the players, if we can keep moving forward and progressing. Off the pitch is a different matter.
"But we are showing a real maturity, a real style and identity of football which is hard for teams to play against, and to come to Cardiff and really dominate the game is a big thing."
Derby have been deducted 21 points this season, 12 for entering administration and nine points for a breach of the EFL’s profitability and sustainability rules during the 2018-19 season.
The English Football League has warned Derby’s future remains in peril as administrators have left phone calls unanswered and failed to provide proof there is funding in place for the remainder of the season.
Administrators Quantuma issued a brief statement on Wednesday morning which said they were “currently considering bids for the club” and hoped to name a preferred bidder “shortly”.
Barnsley travel to Derby on Saturday, with the Tykes searching for a win to continue their revival following two victories in their last three games.
The Reds are two points ahead of Derby, having played two fewer games, but Rooney insists there is still hope for his side.
He added: "It's not over. It's a difficult task now, but we'll keep working and trying to put in performances and pick up points."