Right. Now that you have grasped the meaning of the previous quote you can understand the difference between fiction and reality when it comes to shinobi (another word for ninja). Ninja have always been portrayed as mere technicians of violence, who support any cause for the right amount amount of money. Worse yet, they were (are) mostly portrayed as thick headed fanatics without emotions, always acting the role of cruelty. The truth is far more complex and I cannot claim to have grasped a fraction of the real history of ninjutsu, but will nevertheless, foolheartedly, attempt to give the reader a picture of how it might have been. The people now referred to as ninja did not use that name themselves. They considered themselves to be followers of different social and cultural beliefs opposing those of the ruling class. Ninjutsu was developed as an illigal counter to the ruling samurai caste. Among the practitioners were such elements as Chinise ex-patriots, warriors and scholars, Japanese Taoist sages and from T'ang China, military generals. All these people brought with them a heap of knowledge from India, Tibet, Eastern Europe and Southeast Asia which became the foundation of Ninjutsu philosophy.
Living far away from the imperial court of the emperor the early families were mainly naturalists and mystics. They remained that way, while the rest of Japan were brought under tight control by the samurai and their lords. Eventually the centers of Ninjutsu became located in the Iga and Koga regions where over seventy families refined the art to perfection while adding their own techniques. The influence by these individual was subtle but effective in assuring the future of their lands and families.
When looking in history books one should not expect to find many references concerning ninja families and their deeds. This is not very surprising as history was largely written by the ruling class, the samurai, who despised the ninja, but nevertheless tried to gain their favors.