No, it was just timing. The AT&T lawsuit cast a palor on the BSDs just when Linux started hitting its stride. By the time the lawsuit was settled, Linux had dominant mindshare.
Same reason why MySQL is popular -- PHP gave it the mindshare. Same reason why PHP is popular -- it was one of the few options available at the time, and by the time better things came along, it was already firmly rooted.
The objective reasons for being not as popular I think, that FreeBSD never positioned itself as a desktop system, and many small things (such as how fast it boots) are neglected. Yet, overall simplicity and order is attractive to me; a lo easier to understand internals IMHO.