Good question!
“Good question!”
As I recall, Trump called what he had done unacceptable. I am sure that Trump got the information he used from a biased or uniformed source. It took years for the real story to come out. If your boss says something like that, it’s time to resign.
Also, the FBI was threatening his son. Even if there is absolutely nothing there to investigate, the fact that there is an investigation is damning.
Flynn was put under extraordinary pressure. I suspect that he felt if he resigned the pressure would go away. It didn’t. It got worse. (Like falling down in front of a wolf.)