Al-Badri stepped down from his role after the Red Devils' 3-1 loss at Ismaili in the Egyptian Premier League on Sunday.
Ahli's performance was particularly lackluster, which urged a host of spectators to jeer Al-Badri and call for his departure few minutes before the final whistle.
Khashaba confirmed that the fans' pressure on the 50-year-old was the reason why he decided to quit.
"He felt that his relationship with the fans was not so good, so he opted to resign before it take a turn for the worse," Khashaba, who also resigned along with Al-Badri's backroom boys, told Ahli TV.
"We faced many difficulties of late. We tried to deal with them but I guess we couldn't.
"Al-Badri did his best and won titles but we are no angels after all. There were some mistakes indeed."
Al-Badri, who succeeded Manuel Jose in the summer of 2009, has been living in the shadow of the highly-rated Portuguese, with the fans consistently drawing comparisons between both men.
Al-Badri was under immense pressure to replicate the heroics of his predecessor.
He was largely unconvincing for the ever-demanding supporters despite winning the league title, a sixth successive one, in his first season in charge.
Ahli said the manager seat will be filled in the immediate future.