I flew a lot last pregnancy, mostly for work. My OB was only concerned about the last couple of months.
Flying in the 1st and 2nd trimester was not a big deal for me. Try to get an aisle seat so you can easily get up and move around and go to the bathroom. Don't forget that you are at higher risk for blood clots while pregnant so just be sure to keep moving.
Also I made sure I brought a big bottle of water (or two!) on board with me because it's hard to get enough from the drink service on board. Either buy water after security or bring an empty bottle with you and fill it at a water fountain.
Now I did also do a business trip to Brazil at 7 months. I had agreed to it at 4 months, thinking it would be more of the same. It was absolute torture. At that point anytime I sat in a normal seat (anything but my yoga ball), it would push DS's feet up into my ribs and cause excruciating pain. So you can imagine that all that sitting on the flights (SFO to Houston, Houston to Sao Paolo, multiple domestic flights in Brazil, and back again) was tons of fun. I couldn't get enough pillows in the hotels to get comfortable at night, and was absolutely exhausted for the work days. Plus it was only when I was on my way there that I had the realization that if something did happen, Brazil was probably not the best place to be, with their 99% c-section rate, so that was stressing me out.
No more long trips (and preferably no short trips) in the 3rd trimester for me anymore!