@David09 - I think I know what you’re talking about; the book you’re referring to stirred some controversy.
But you raise a good point-when Darwin was around, there was no such thing as molecular biology. A simple cell was viewed as a simple cell. With the power of the electron microscope, we can see that it is anything but simple, and that in fact molecular biology would suggest a different family tree than what Darwin could have anticipated.
After all, his classifications were made as a result of purely visual observations, nothing happening at the molecular level.