As it is with anything in your pregnancy, the ultimate choice is always yours to make. Airlines can not legally refuse a pregnant woman as it against human rights, however your insurance might not be valid after a certain gestation so check with your insurance company if you need to disclose your pregnancy. You will also need to consider on where you are travelling to and what that countries medical facilities, hygiene levels or any known diseases you may be exposed to just as you would if you were not pregnant and then make an informed choice that you are happy with. Remember that pregnancy is not an illness however you may (depending on the airline) need to provide a medical certificate stating that you are fit to fly, even on domestic routes, so please check the fine print of your chosen carrier.
With long haul flights, when pregnant there is an increased risk for developing a deep vain thrombosis (DVT). Pressure stockings, in flight exercises, walking around the plane, avoiding crossing your legs and ankles, and drinking plenty of non carbonated water will help to reduce this risk. You must seek immediate medical attention if you experience any calf pain or calf throbbing or shortness of breath.