Business adviser firm Quantuma were put in charge on Wednesday, triggering an automatic 12-point deduction.
Asked whether he would have taken the job if he had known about the financial problems, Rooney said: "I doubt it."
But the 35-year-old added: "I am here to fight for the club and the staff. They need someone to lead them."
The Rams secured their Championship status on the final day of last season, and have won two and drawn four of their eight league games so far in 2021-22 despite being subject to a transfer embargo which meant Rooney was only able to recruit free agents.
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