I flew every 4-6 weeks of my pregnancy. Including Hawaii at 30 weeks, across country (to be a bridesmaid) at 33 weeks, and finally a short 45 minute hop at 36 weeks. I was fairly small but I never had any issues. No one even asked how far along I was for any reason other than being friendly.
If the flight was over an hour (most are), I just got up and walked around. I drank plenty of water. I never had problems with my belly in the way or anything.
And for full disclosure, I had a really awesome pregnancy with no complications. I'm sure my answer would be different had my pregnancy been not so easy going.