More mucus is produced if you have allergies. wouldn't more mucus production offer more protection against pathogens? since that is the job of mucus.

Good question: Although it is true that the mucous blanket which is formed by secretion from goblet cells and mucous glands in the upper and lower respiratory tract move potential pathogens out of this respiratory tract, excessive mucus from allergy or other diseases that increase mucus production will inhibit this muco-ciliary movement and actually make you more prone to disease because of impaired cilia.