The Potters went into Wednesday's fixture having only recorded two points from their opening three matches in the Championship, and the Staffordshire-based outfit were well beaten by the Latics at the bet365 Stadium.
Rowett has acknowledged that he could understand the reaction of the club's supporters, admitting that his new side 'have not been good enough' since the start of the campaign.
The 44-year-old is quoted by Sky Sports News as saying: "I'm not going to try and justify any of that. We got the reaction that we absolutely deserved, I'm not going to absolve myself from that, we deserve to be booed, we deserve the stadium being half empty as we haven't been good enough.
"I've got to say to them that I can completely understand their frustrations. I'm not sure whether you can say it was far worse than lots of games last season, it wasn't a good game and I don't think there have been many good performances for a long time."
Stoke currently sit in 22nd place in the second-tier standings.