One of the most successful and widespread schools of Japanese martial arts in the United States is the Bujinkan, the “Ninja school” of Dr. Masaaki Hatsumi. The Bujinkan is actually so successful around the world that many practitioners assume it must be an important school in Japan as well. In reality, the Bujinkan has always been an outlier in Japanese martial arts circles for a number of reasons. One is the historical attitude of contempt some samurai held for the ninja, so that the mere fact of claiming a “ninja connection” is seen as somewhat dubious by those who identify with the samurai traditions. Another is the fact that the Bujinkan's historical claims to a ninja connection have never been proven and are still highly controversial. Another is the structure of the organization itself and how the core curriculum is taught, which is rather unlike the practice in most traditional Japanese martial arts schools.

The Bujinkan is not just Ninjutsu- in fact it contains teachings from nine distinct traditions of Japanese martial arts, of which most are of samurai origins. Some of the schools taught within the Bujinkan still exist as independent traditions outside the Bujinkan. One of these is the Kukishinden Ryu, and if you compare videos of the traditions of this school with the version practiced in the Bujinkan, the differences are remarkable. Here's the Kukishinden Ryu itself:

As you can see, the two don't really seem like the same martial art at all. I'm not qualified to address the reasons for this, but the differences between Bujinkan and more traditional Japanese martial arts is probably the main reason why the Bujinkan has had most of its success outside of Japan.