The point is that neither Kepler, Michelson or Morley started from scratch: They tested their hypotheses, built on observations. Since scientific observations suggested that orbits were perfect circles, Kepler went with that. Likewise, since scientific observations showed that whenever something was moving, it was carried by something (e.g., sound through air), the hypothesis of an aether was suggested.
The difference lies in how the observations have been achieved: Do we rely on people imagining that a chariot drags the Sun across the sky, or do we rely on the scientific explanation, based on logic, rationality and sound models?
Perhaps, that was their "scientific" context for explaining the event at that particular time. Applying a literal interpretation (today) of yesterday's context may be somewhat problematic when you consider the possibility that tomorrow's science may render today's version archaic in application.
That's why Shermer is right: We should start with the idea that we are wrong, and seek to find out what is real, instead of what our senses tell us. There has to be positive evidence - not belief that needs to be disproven.
If the latter was true, psychics would be real, until proven false. Ain't working that way.
