City took an early lead through an Antoine Sibierski free-kick but a mix-up between Jihai Sun and David Seaman gifted the Belgians an equaliser just minutes later.
Sylvain Distin then completely missed a routine clearance from a cross, allowing Runar Kristinsson to put Lokeren ahead on 40 minutes, against the run of play.
But at the break, instead of criticism, the City boss was looking for support.
"We needed the crowd to get behind us but they booed us off in our own stadium. I find that terribly disappointing," Keegan said.
"They were starting to get to one or two players. It is not what you need when things are not going your way.
"I have never had a team which has been booed off before. Even when we were 4-0 down against Arsenal last season that didn't happen. If players are not trying I won't protect them but they were working really hard and didn't deserve that treatment."
Keegan added that City's keeper even apologised for his part in the first goal.
"He came in to say sorry at half-time but said we had to put it behind us," said Keegan.
"The man who hasn't made a mistake hasn't been born yet but it would be harsh to blame David for that goal. There were a few problems before it got to him."
"We didn't get out of jail because we dominated the entire match. They came here with a game plan and worked really hard but they only had two chances.
But Robbie's Fowler strike, although somewhat fortunate, was a bright spot for Keegan who had put the presure on the striker to perform earlier this week.
"I was especially pleased for Robbie because strikers live for goals. That is what they are judged on and hopefully it will give him a lift."