Years ago, I flew while congested and didn't take any medication. It was torture on the ascent/descent. When I got on the ground, I couldn't hear out of one ear for the there days until I got back onto a plane. Interestingly, once we got to altitude on that second flight my "deaf" ear equalized and all sorts of brown(!) fluid drained from my nose.
Sorry for the nasty description, but by all means take medication.