That sentence sounds very suspicious to me. When refering to single sentence to make a point, the person usually ignores that the author gives as evidence of certain event without any witness.
For example, a forensic scientist, on the stand, could be asked by the defense attorney if there was any witness that could testify that the defendant raped and killed the victim, and the scientist says "no, but..." and the defense goes "thank you very much. No further question."
What the defense attorney is doing is suppress information. The scientist was going to say "no, but we found the defendant's sperm sample in the victim, his finger prints were all over the victim's clothing, and his saliva samples were all over the victim's face."
Going back to your quote there, of course noone saw the evolution of one toed horses from three toed horses. If anyone ever claim that he saw such an event happening, he belongs in a mental institution.
"...but that does not mean we cannot be confident that horses evolved" sounds to me like the author have already or will give evidence to support his belief in such an event taking place.
Without the rest of the texts, I can't really answer your question.
The Laminator