I have never seen a book, especially a science one, with such a bimodal response. IMO, the people with one star were trained as biologists. They present a valid viewpoint--I'll get back to that later.
When I first read this book at the end of my undergrad days, I was simply amazed. I never realized biology could be so fun, if we asked questions about robustness, optimality, design principles, etc. Now that I'm in this field in my day job (as a grad student), I realize this book does have some issues.
First, the book does make some strong claims, ie. the idea of inherent design principles. This is what most of the one-star reviews here are angry about. Alon doesn't really discuss the philosophy behind systems biology, but jumps straight to the physicists' view that the system is understandable and our job is to understand it.
Also, the book pretty much only covers work done by people in Leibler's lab. The works presented in the book are considered hallmarks in the field of systems biology, but people familiar with the field might be sad to see some areas not presented here.
Finally, it should be noted that the book doesn't really teach you that much. It does a wonderful job telling the story of the papers that it does discuss, but it hides away the details. Thus, you don't learn the biology of what's going on nor will you learn common mathematical techniques used in this field (eg, bifurcation analysis).
Nonetheless, I give this book five stars enthusiastically. This is the most enjoyable book I have read, and I highly recommend it to everyone who has any interest in this field. The problems included in the chapters are not bad for use in a class, although I recommend Strogatz's Nonliner Dynamics for a class focused on the modeling.