The problem is that these are two entirely different things:

(A) Using torture to extract life-saving information from somebody whom you already know by OTHER means has the information you're looking for and is unwilling to divulge it. (The example Sam Harris used was that you caught the guy who planted a time bomb which has not gone off yet, and he's already admitted that he's the one that planted it, and now you're just trying to figure out where the bomb is and how to diffuse it.)

(B) Using torture to extract allegedly life-saving information from somebody whom you are still merely alleging has that information you're looking for, but you don't know that yet. Then using their confession and divulging of information under torture as evidence that your claim was right about them.

The problem is that Sam Harris made his statement, which was about scenario A, during a time in which the US government was using torture under scenario B, and scenario B is what was foremost in their minds at the time they read his book. They assumed he was talking about B, but that he was being dishonest about it and falsely portraying it as scenario A.

In other words, they took his hypothetical case as if it was his attempt to describe the actual case that was going on at the time and whitewash it to make it look better.