For starters, who are you talking to? I for one am not really a fan of Shelby Foote. His narrative style is certainly to be commended, but from the standpoint of a historian his major work, while massive, is largely lacking.

Generally speaking, Foote has a poor reputation among historians because of his lack of footnotes which make his sources difficult to track. He has also been accused of pro-Southern bias in the past as well as taking liberties with his narrative (read: stretching the truth or making things up, depending on who you ask). Even if we give Foote the benefit of the doubt on issues like bias or integrity, the fact remains that much of his work and the historiographic base he relies on is now ridiculously out of date. The first volume of his narrative came out in the late 1950s and Civil War scholarship has undergone massive changes in that time. This lacking is no fault of Foote's, of course.

Anecdotally, I've never met any historian who would recommend or accept Foote as a scholarly source of information. One adviser actually laughed out loud at the thought. If there is value to be found in Foote's work in the present day, outside of it just being a fun read, it would be the massive amount of detail he offers that just can't be found very often in single works. But the difficulty in verifying his information (as in, no footnotes) leaves this very questionable from a scholarly standpoint.

GG&S is also not a scholarly work, it uses the wrong style of language, several of its claims are backed up only with observation giving it a feel of a version of the anthropic principle all of which make it easy to dismiss and attack.

That you have a non-historian coming in and attempting to explain a major historical event, using completely different set of theories and science that at a technical level they cannot understand without large amount of new education and that GG&S pushes against a lot of the current trends in how history is written and approached, it tackles epochs from prehistory to the modern era a book of this type will run against psychological aspects of changing long help opinions in any field. Anything work of this type will generate a visceral re-action, and coupled with the softness of the text that feeling is easy to justify.

GG&S is not a definitive work, but it raises questions around the degree that geography, climate, molecular biology, and evolution effect the course of history.

I'd like to know more about the unreliability of Guns, Germs and Steel - I remember I enjoyed the book, so I'm worried if I learned something wrong.