Should a cover letter always be included in faculty job applications?
The cover letter is one place in your application where you can explain why you're interested in this particular position including both professional reasons ("I'd really like to work with your library's archive of original manuscripts by P.D.Q. Bach")  and personal reasons ("My in-laws happen to live in your small town and my spouse would like to move back.")  Showing that you know something about the location, the the institution, and the particular position can be a helpful factor if you're on the borderline for an interview.  

If there's really nothing special that you want to say then a generic two sentence cover letter won't greatly hurt your chances.