I don't think you can treat those as equivalent. The arguments against airplanes were about physics, which is comparatively easy. The whole point of this essay, and KSR's companion novel Aurora, is that people who get excited about generation ships tend to only think about the physics and engineering problems, and handwave away the problems of ecology, biology, sociology, ethics (!), and politics (!!) because they don't find them interesting, even though these problems are actually much harder to solve. His complaint is that by sweeping the hard problems under the rug, people are making this out to be a much more feasible operation than it actually is.

In order to prove him wrong, you'd have to really grapple with the question of how to have a self-sustaining ecology in space. This is something I basically never see in online space boosterism, and note that empirical attempts to answer it like Biosphere 2 ended in complete failure (and those were on Earth, which is orders of magnitude easier).