no, you definitely should check with your doctor if you're getting sick. If you fly with an ear infection, you can permanently damage your ears. That's what I had to do before I went away...but the flight was still torturous on the ears.
I think I have some type of medical problem because my ears hurt so bad last time I flew that I almost started crying. I didn't have an infenction it just felt like someone was sticking needles that were on fire in my eardrums the whole time.