However, I don't know why the author would even suggest that annotations are innocent looking. They aren't any more 'innocent' than an if statement. Something like: 'if (myMethod())' could easily be a long running database query or call out to a fibonacci solver. Should we all be afraid of using if statements too?

I'm sorry, but there is really nothing 'magical' about annotations. It is simply a marker on a class, property or method that other code can read from and do things with. Prior to annotations, apps were processing Javadoc (@see early versions of GWT), which was an even more terrible idea since you didn't know if it was Javadoc or an annotation.

The summary is that a) software engineering is not easy and it does involve knowing what you are doing in order for things to not appear 'magical'. b) If you are going to put an annotation on something, then you should know what code is going to read that annotation and what effects it might have. That said, that isn't the fault of the annotation language feature.