Millwall were welcoming supporters back to their ground for the first time since February, with 2,000 in attendance in south London for their first home match since the second lockdown ended.
But their appearance, and Derby's 1-0 victory, was overshadowed when a section of the crowd chose to boo both sides as players showed their support for the Black Lives Matter movement for racial equality.
Twenty-one of the 22 players who started the game took the knee with the other, Derby's Colin Kazim-Richards, raising his fist.
"I'm sat here as a manager disappointed that we're not talking about the game," said Rowett.
"I think the club have done so many positive things in the community related to anti-discrimination through great initiatives.
"It's a club that works incredibly hard to enact change and do something about situations we all feel we need to be more proactive on.
"We're all disappointed we're having to come in and talk about it."
However, Rowett revealed his players feel more can be done to tackle discrimination and racism.
He added: "The players have released a statement together and said they don't support it [taking the knee] as a political message but support anti-discrimination.
"Moving forward, like a lot of clubs, they would prefer not to take the knee and actually enact change.
"They want to be proactive rather than it being a gesture, which a lot of clubs are now saying is perhaps empty.
"That's not my consideration, but they now feel that gesture is in danger of being empty."
The incident cast a shadow on what should have been a pleasing day for Wayne Rooney, who celebrated his first win as Derby's interim manager.
Jason Knight's second-half strike allowed the Rams to record just their second Championship triumph of the campaign, and the first since Rooney took over last month.
But talk after the match was focused around what happened before a ball was even kicked.
"I heard it and was very surprised. It's a sad thing to happen but all I can say is everyone involved at Derby County Football Club has fully backed taking the knee and will continue to do so," said Rooney.
"It's a shame because there has been great progress in that campaign and hearing that is very disappointing and upsetting for a lot of people.
"I'm pleased with how my team dealt with that because I'm sure they put it to the back of their minds during the 90 minutes.
"I'm sure it's something that does need looking at and addressing.
"I could see the team progressing in a very good way coming into the game.
"I'm delighted with the clean sheet, which has been long overdue, and getting the three points was deserved because of all the effort the players are putting in on the training ground and in games.
"It's really pleasing, gives us something to build on and will give the players great confidence.
"I'm delighted for everyone at the club because it has been a difficult time."