haven't seen anything about him that makes me believe he wasn't just a spectator. remember when we were in the mud with MSN and after a whatsapp chat the boys rallied to make lucho a treble winner? that's what happened to flick also. the squad was there, it's not as if he did something spectacular. bayern had the ability to dismantle teams before flick came in.
In his first 16 matches in bundesliga bayern scored 50 goals, average 3.1 goals per game - best in history of bundesliga football. I cant find a pic which shows the amount of chances created between kovac and flick but if you would have saw the matches you could have seen clearly a difference between both Bayern's - Flick Bayern has created a lot more chances.
To say that he just won because of the squad is no argument, why didnt kovac win in previous year? He had the same team but they looked like a harmless cat in attack against liverpool in both matches and scored only one goal (own goal). That Liverpool wasnt even impressive but Bayern managed to be a lot worse. By the way you could say same about Pep according to your logic: he did do nothing, only played the best football in history because of the squad.
Edit: In season 19/20 Kovac: 5 wins, 3 draws, 2 losses: 1.8 points per average ---> Flick 2.43 !
Under kovac offense: 2.5 goals per average ---> under Flick: 3.3 !