Q: Is it okay if the Imam makes qunoot in Fajr prayer? If not, what should I do? The Imam makes it everyday.
A: It is disliked to make qunut in the obligatory prayers including Fajr. The only exception is the main Imam (the ruler) during times of great strife and hardship. He is recommended to make qunut in the obligatory prayers except for Jumuah. If you find yourself praying behind an Imam who regularly makes qunut in Fajr, you should follow him. The Imam was made to be followed and so you should raise your hands to supplicate and say 'Ameen' after. Source: Sharh al-Muntaha