I have nursed on airplanes several times and have never had a problem. I have, however, always flown with my hubby, too, and he sits in the middle seat while I sit by the window. I think it's key to get an airline blanket or pillow or bring your own to rest baby's head on so they don't hit their head on the hard armrest or wall (this has NOTHING to do with covering up - just protecting baby's head!)
Finally, I think it's important to realize that ears pop when going up and coming down, so those are the best times to nurse, feed a bottle, give a sippy cup, or a pacifier - whatever to get the baby to suck and swallow to minimize the pressure in their ears.
Happy Travels!