Haven't read the book, but I know caffeine is no miracle drug. It's a great drug, and very healthy. But it has plenty of adverse side-effects, especially at the high end of consumption. Not to mention withdrawals. My life is best when I drink it about once a week.
Don't forget, Dave makes money off the demand for coffee...
Haven't read the book, but there are thousands of PubMed papers, books, forums and such that speak positively about coffee, just as there are other sources that speak negatively about coffee. It's good to get educated in a variety of subjects/opinion, so expose yourself to a variety of sources.
I roast coffee, drink coffee and feel I understand how coffee impacts me after years of observation and trending. Like all things in life, whether it is drinking BP coffee or eating dirt from your backyard, you should pay more attention to your own observations and trending rather than other people's opinions on what should or shouldn't happen to you.
I like to rationalize the effects of caffeine as a "shift." It allows me to do some things better, and other things are more of a challenge. Why ignore the positive benefits of caffeine? Why ignore the negative? Just like Staylor says about the PubMed studies, take a closer look inside and see what is going on and how you respond to it. Learn how to use it as a tool. Or, if it's not your thing, cut it out.