There's no need to leap to 'idiocy', it could mean the people struggling with weight have either poor willpower, or honestly don't know how to eat well. You can see this by watching shows like 'Secret Eaters' and seeing how incredibly common it is that people are over-eating and just don't realise it.
And researchers will research wherever there's funding/academic opportunity.
Clearly a lot of factors have changed in 100 years, like our now abundant, convenient sources of calorie-dense food, and sedentary lifestyles, which mean our knowledge and willpower are now more significant than they were then.
Peer pressure and advertising allow for many other possible explanations.
One thing I thought Taubes did a good job of was illustrating the relationship between calories in and calories out: your body will burn more calories when it has them, and less when it doesn't. You will be hungrier when you burn more calories, and less hungry when you don't. Calories in isn't just a knob you can adjust without consequence, your body is complicated.
For this to be true, it would have to be true that the millions of people struggling with weight, and the tens of thousands of researchers in the field, are all simply idiots who are not as smart as you.
The people who say "Calories In < Calories Out, it's simple" are about as helpful as the client or exec who says "It's just code, change the code and don't write as many bugs. It's simple"