The period since 1992 was relatively peaceful, that's right. But that's not what Fukuyama's thesis was about, especially since he couldn't know in 1992 what would happen in the next 30 years.
Fukuyama's theory was that mankind has reached its optimal, stable state and that that the further historical changes are very unlikely, because why would people want to mess with perfection :) It was basically very naive optimism, I guess he was still in euphoria after Soviet Union collapse...
Since then we had "war on terrorism" and PATRIOT act, big financial crisis of 2008, rise of social media and surveillance state, and now COVID pandemic. Plenty of historical changes, most of them for worse.