Flores defended his decision to play eight consecutive Jay-Z songs during Tuesday's practice, the day after Stills took issue with Roc Nation's NFL partnership.
"It was a challenge to Kenny to perform regardless of whatever is going on outside," Flores told reporters, according to ESPN's Cameron Wolfe. "I would say, and I said this to him, he hasn't performed up to that level over the course of training camp, or as I've seen. So that was the challenge - to get open, catch the football, and make plays for this team, regardless of what's going on outside of this building."
Stills believed Jay-Z "could have reached out to Colin (Kaepernick)" before finalizing the deal and stated the rapper could not relate to the protesting players.
Surprised by the media attention the incident received, the first-year coach made sure his team understood he supports Stills and other players who choose to take action.
"Quite honestly, they're bringing attention to my story," Flores said. "I'm a son of immigrants. I'm black. I grew up poor. I grew up in New York during the stop-and-frisk era. So I've been stopped because I fit a description before. So everything that these guys protest, I've lived it, I've experienced it. So I applaud those guys' protest.
"So whether it's Kaepernick, or Eric Reid, or Kenny, I applaud those guys. I told Kenny that in our meeting in front of the entire team."
The veteran receiver acknowledged the two handled the situation personally and insisted there were no hard feelings between him and his head coach.
"We talked about it in-house and he handled it in-house," Stills said. "For the most part, I think it was him seeing if I could handle if people were going to heckle me or play Jay-Z in another stadium if I could be mentally strong enough to handle that sort of treatment. I've been dealing with this since 2016 -- music, boos, racial slurs. So I don't think a little Jay-Z music is going to ruffle my feathers that bad."