Be careful with your preceived opinion from your boss. Most of us started with the same perceptions, but after time, realized the our bosses and management really do not care. I have been in a management position before, and believe me, there are much larger issues to address than an employee's facial hair. Even an occasional negative comment from a manager would not give me cause for concern now that I have been bearded for a few years. Such comments usually are not a hidden directive for a guy to shave, but just a random comment. If a manager wants you to shave or "clean up" he/she will directly tell you so there is no missunderstanding.

My Beard Journey:  http://jefffsbeardboard.yuku.com/topic/25137/Finally-I-have-a-Beard
Beard and Bald Thread:  http://jefffsbeardboard.yuku.com/topic/27831/Beard-bald-head-shaved-head-or-buzzcut
Patchy Beard Success Stories:  http://jefffsbeardboard.yuku.com/topic/33742/Patchy-Beard-success-stories-Before-and-After-photos#.ViujbH7nuM8
Taming the Wild Mustache:  http://jefffsbeardboard.yuku.com/topic/30822/Taming-the-Wild-Stache#.Vj_Mh7erTIU