Some interesting views, on reddit
"Homo-" means "the same", and "iso-" means "equal".
Something homogeneous is "the same throughout" rather than "equal throughout". Something isotropic gives "equal measurements in different directions", rather than "the same measurement in different directions".
The difference in meaning is kind of subtle, but it's there.
iso- from Greek isos equal
homo- via Latin from Greek, from homos same
One would therefore expect words of Greek origin to take the iso- prefix and those of Latin origin take the homo- prefix. (Does that hypothesis hold?)