I flew in my second trimester and was fine. Had no probs whatsoever. A couple of weeks later there was a possibility that I needed to fly again, and I needed to change my docs appt. When my doctor heard about this she insisted on examining me and giving me a docs note that I was OK to fly, even though I was nowhere near the cut off point for flying - think sometimes they are a bit OTT over here and want to cover themselves!
Different airlines have different cut off dates for accepting pregnant women, some say 28 weeks, some go to 32 weeks with an accompanying docs note. Check with the airline you want to fly with.