To use a humidifier or not?

My almost 3 month old has had a horrible wet cough for over 2 weeks now. I have gone to the doctor twice and he said it's just a common cold so keep the humidifier going. I've noticed during the day when we are away from the humidifier she rarely coughs. At night when she is sleeping, the doctor said to keep the humidifier on high by her. She wakes up coughibg, gagging, and has trouble breathing. I want to quit using it at night but the doctor says not to. I just feel like it makes it 10 times worse for her. What would you do?