Flores expressed support for Tagovailoa on Monday and avoided singling him out, focusing on the team's collective effort instead.
"We all have to play better. We've got to coach better. He's not in this alone. He's got my full support, he's got the support of our coaching staff, he's got the support of every player in that locker room," Flores said, according to Sports Illustrated's Alain Poupart.
Tagovailoa was benched for Ryan Fitzpatrick after completing just 11 of 20 passes for 83 yards. In his fourth career start, he was also sacked six times.
Fitzpatrick threw for 117 yards in relief, but his late interception sealed the Broncos' victory.
Flores said afterward that Tagovailoa would remain the starter.
"He's the starting quarterback. He knows that. We've had that conversation. He's played well. And I expect him to continue to play well, I expect him to bounce back," Flores said. "He's a resilient kid, like I've said. ...
“Look, this is clearly a very talented player. He's played well. He's a young player and he's an improving player. And he's a developing player. We've got a lot of confidence in him."
Tagovailoa has led the Dolphins to a 3-1 record since being named the starter. The former Alabama product has yet to throw an interception this season but is managing just 120.4 passing yards per game.