The issue with Lathrop's books, from the perspective of a historian that takes history seriously, is that they are in large part folklore. The average reader might take the entire text at face value and say "yes, this is true" and leave it at that.
There is no doubt that what Gilbert Lathrop wrote about his own experiences are true. What he wrote about his father is one degree of separation as he is writing what he remembered his father telling him. What he writes about
history is where you run into problems. Lathrop didn't write as a historian, he wrote as a chronicler of oral tradition on the railroad, and the "history" he recounts isn't necessarily the history that external records can verify.
Note that
two threads have been started this year so far asking for more detail about Lathrop's claim that the Garfield Monument was actually built as a monument to the casualties of the passenger wreck, but then backtracked to commemorate Garfield's assassination to avoid "embarrassment" to the railroad company. Nobody has been able to provide any other documents to back that up, and the derailment didn't even happen at Rock Tunnel, and was not quite as dramatic as what Lathrop wrote down. This is an example where the book strays from history and becomes folklore. No doubt this is what he and his fellow D&RG employees believed was the story, but it doesn't necessarily mean that it was the true story.
I think what MatthewM is saying is that many of these classic books need to be read with a critical eye, not necessarily that they need to be thrown in the garbage and ignored.