I currently have pharyngitis, went to the dr 3 days ago. My throat and congestion is getting better but my ears seem to get more and more plugged. Why?

Connected. Ear nose and throat are all connected. Sometime inflamation of the throat will cause blockage of the eustachian tube which will give you these symptoms of ears popping and getting plugged. Steam inhalation and a humidifier at home will help with these symptoms. If your ear hurt or if you have a fever, get back to your doctor.