For a number of reasons, BSD is relatively unknown:
The BSD developers are often more interested in polishing their code than marketing it.
Much of Linux's popularity is due to factors external to the Linux projects, such as the press, and to companies formed to provide Linux services. Until recently, the open source BSDs had no such proponents.
BSD developers tend to be more experienced than Linux developers, and have less interest in making the system easy to use. Newcomers tend to feel more comfortable with Linux.
In 1992, AT&T sued BSDI, the vendor of BSD/386, alleging that the product contained AT&T-copyrighted code. The case was settled out of court in 1994, but the spectre of the litigation continues to haunt people. As recently as March 2000 an article published on the web claimed that the court case had been “recently settled”.
One detail that the lawsuit did clarify is the naming: in the 1980s, BSD was known as “BSD UNIX®”. With the elimination of the last vestige of AT&T code from BSD, it also lost the right to the name UNIX. Thus you will see references in book titles to “the 4.3BSD UNIX operating system” and “the 4.4BSD operating system”.
There is a perception that the BSD projects are fragmented and belligerent. The Wall Street Journal spoke of “balkanization” of the BSD projects. Like the law suit, this perception bases mainly on ancient history.