I think it should be fine. I was just diagnosed with a 5.6 cm cyst and am flying to Europe in 3 days. My doc wasn't concerned about the long flight.
I don't think it would be a problem. There are activities far worse than flying that could cause a cyst problem to worsen (jiggly motions like horseback riding for one). I cannot see how sitting or even air pressure changes would make an impact.
Flying after cyst surgery can sometimes be a problem because of post-op risks of dangerous blood clots....sitting idle on a plane for long stretches tends to also increase the risk of harmful clots. When I was recovering in the hospital I heard the story of a man that did not survive appendix surgery because of a post- op blood clot. That is why a good hospital takes so many precautions to prevent dangerous clots from occurring.