It's just a simple analogy that quickly breaks down.

The frogs have it easy. All they have to do is jump out. One individual action and they're safe. (Until the scientist catches them and uses them in more experiments, anyway.)

The situation for people living under governments becoming gradually more oppressive is much more complicated. You don't know for sure that the water will keep heating up. Escape is extremely difficult and costly. Turning off the heat takes massive collective action. A third of the frogs actively want the water to boil, and another third don't really care.