Pulmonary emboli are caused by blood clots that form in the veins, usually the deep veins of the legs, but occasionally veins in the pelvis. These clots then break loose and travel through the veins to the heart, where they are pumped out to the lungs. Small emboli are rarely noticed, although if they occur in large numbers they can cause problems. Medium-sized emboli will block a branch of the pulmonary artery, and cut off the blood supply to a segment of the lung. This may cause the death of some lung tissue, termed a pulmonary infarct, and although this may be painful, it is rarely fatal.
Large emboli can block all the blood flow to both lungs and are rapidly fatal.
Over the years, we have learned more about the formation of such emboli, and forced inactivity in a sitting position is one of them. It's unfortunately all too common in economy class with the crowded seats, narrow aisles, and limited opportunities to move about. It's also significant that we don't hear about this problem occurring in business or first class seats, where passengers legs can be raised higher, and the wider aisles allow people to stretch. Other conditions including some cancers can also lead to a hypercoagulable state. Orthopedic surgery, especially on the hips or legs can increase the risk of thrombosis for several months.