Maddon was "surprised" and didn't "really understand" why Hurdle criticized Baez. He also said he believes "in not interfering with other groups."
"Be careful when you start becoming hypercritical because you're pretty much defining yourself," Maddon said prior to Friday's game against Atlanta.
The 25-year-old Baez homered twice for the second straight day in Chicago's victory over Pittsburgh on Wednesday. But he also flipped his bat high into the air on a popup to shortstop Jordy Mercer in the seventh inning.
Baez acknowledged after the win it was a mistake and that a teammate talked to him about the display.
Hurdle questioned Baez's "respect for the game" on Thursday, and the flashy star brushed off those comments after the Pirates beat the Cubs.
Maddon praised his player for owning up to his mistake. He also said he didn't see the bat flip.
"I think most of the time when you hear commentary — or critical commentary — it's really pretty much self-evaluation," Maddon said. "It's about what you believe. It's about your judgmental component. It reveals you more than the person you're talking about. I've always believed that. Whenever you want to be hypercritical of somebody, just understand you're pretty much revealing yourself and what your beliefs are."