I think the problem lies in that, unless you do some research on what school/style's afiliation/roots are, you might genuinely think you're studying an ancient form of Gimme Yo Mani Jujutsu, only to find out later after having spent precious time and money, that the instructor made up the style based on a few weekends worth of judo classes at the YMCA. So, as a result, people's respect for traditional jujutsu (or traditional martial arts in general) begins to erode.
Not that I have anything against the YMCA (I spent several years training in karate in one) . . . it's just that, from a standpoint of a newbie with zero experience, whose word do you go by? Do you follow the marketing ads, "My Jiu Jeetsue is strongest!" in the yellow pages and internet? Do you listen to your friends? How do you know if you're doing the real stuff? I think we're going to see, if it's not already apparent, a number of people claiming to teach BJJ, then being revealed as being fraudulent. I can see it now, "Fernando Chiquita, heir of the secret system of Portugese Jujootsu".
How does this relate to traditional jujutsu? Well, if you're trying to learn an older style of it, how do you go about finding a teacher? Being in the United States, there are only a few koryu exponents that I know of that have spent time in Japan learning their stuff -- Meik and Diane Skoss, Ellis Amdur, Phil Relnick . . just to name several. Chip Armstrong is the current director of the International Hoplology Society, which was founded by Draeger, and maintains a website at .http://www.hoplology.com
Diane Skoss also maintains an excellent website Koryu.com which has many articles that detail some of the catalogued Japanese koryu. Her 'Classical Warrior Traditions of Japan' Series (of which, I believe, there are three volumes) that she edits do an excellent job of continuing the work begun by Donn Draeger in his original volumes. As ronin69 pointed out, many of the koryu are battlefield systems that address weapons and empty handed techniques .
My own feeling is that it's very important to be familiar with the ranges of unarmed engagements, e.g. if someone shoots in for your legs, kicks at your head, throws
a fast hook or tries to choke you out -- none of these things should be experienced for the first time on the street. The dojo is the place to learn without fear (hopefully) of permanent injury. I also think that nothing makes you appreciate distance and timing like someone swinging a weapon at you.