Ninjutsu is NOT the art of assassination.
Ninja's do NOT do spinning back kicks while somersaulting through the air despite what some so called Sensei Master's will tell all who are stupid enough to believe.

Most of our teaching tells us that the Ninja lineage probably originally came from the Yama-Bushi.
These warrior monks originated in Kyoto region, which at the time was heavily Shinto dominated, but also later became integrated with Buddhist beliefs.

Because one of the main practices that the Yama-Bushi trained in was the fighting arts, their numbers were often swelled by the influx of 'Sohei', who were often peasants, and this made the monasteries "armies" grow to considerable size.
The priests were originally called 'Gakusho' but the name that stuck was Yama-Bushi (mountain warriors) due to the fact that they came from Mount Hiei The term Yamabushi was/is the name of a sect of Buddhist priests and literally means 'mountain sleepers', although written with different Characters.
Buddhism was originally introduced in the 7th century but was not popular until it was re-introduced by Eisai in 1192.

Another source of the origin of the Ninja came to be during the 11th Century at about the time the Samurai came to power. The Ninja decided that they did not wish their lives (and deaths) to be controlled by some all powerful warlord.
The Ninja relocated their families to the mountain regions in Japan and set up a counter culture. Here, all the family members worked for the good of the Clan.
In order to protect their families the Ninja developed many skills. Expert fighters taught Martial Arts (Tai-jutsu), Great riders taught Horsemanship (Ba-jutsu), and the Learned taught Academic and Science skills (Ten-mon, Chi mon).
The Ninja also became experts in explosives (Kayku-justsu), as well as many weapons. In fact, of all the Martial arts Ninjutsu has the most diverse array of weapons.
The Ninja believed that learning was for everyone and not just the rich. Children were taught the same skills as adults. The Ninja were also great Philosophers (Kyojitsu Tenkan Ho).

Because of all these skills the Ninja became feared warriors and tacticians. The warlords who had even one Ninja in there employ were deemed to be powerful and dangerous.
These skills and powers became the eventual downfall of the Ninja.
By the 17th Century, the Warlords and Samurai had become so afraid of this alternative society that they set out to destroy the Ninja completely.
The stories of these "wars" are legendary and are told elsewhere on the web and in many books. As testament to the power of the Ninja it cost the lives of many thousands of Soldiers and Samurai before the Ninja were beaten.
It is believed by many that the surviving Ninja simply went to ground living their lives in secret, indeed the proof of this fact is that Ninjutsu has once again risen to be seen now, not just by the Japanese, but by the whole world.

And yet another type of Ninja is found amongst the Samurai. The most famous Ninjas of all were Samurai who were specially trained to conduct missions in secret and to destroy the enemy in a way deemed to be not honourable and as such it was never admited at the time that Samaurai had commited these acts. 

And so in conclusion, we can see there is are three definate and seperate origins of the Ninja. 

When you visit a Dojo do not expect to be taught Ninjutsu in the old ways. How many Dojo's can truthfully say that they have Horses, Yari, Naginata, Explosives, etc. or even that the Sensei would know how to use these themselves. The art of NINJUTSU covered all of these things and much more. The term Ninjutsu has now been replaced by Budo-Taijutsu in both the Bujinkan and the Genbukan due to the fact that this is perhaps more accurate as only 3 on the 9 schools taught in these dojo were Ninjutsu Ryu

What you should expect to be taught at the very least is :-

Tai-Jutsu......................Unarmed combat, including Daken Tai-Jutsu (Striking, Kicking, Blocking), Jutai-Jutsu (Grappling), Nage Waza (Throwing Techniques), Taihen-Jutsu (Silent Movement)

Kaiten...........................Rolls

Junan Taiso...................Body conditioning

Bo-Jutsu.......................Stick and Staff fighting

Ken-Jutsu.....................Sword techniques

Seishin Teki Kyoyo.......Spiritual refinement

These are the BASIC TECHNIQUES. If your Instructor does not teach these things ask him/her why ?
Have you seen your Instructors certificates ? Do you know who his Teacher is ? Have you trained with his Teacher ?
Ask questions and ask more. Have you tried other Dojo's ?
If you are going to learn NINJUTSU make sure it is NINJUTSU you are being taught.