Fair use absolutely does extend to commercial works such as novels. That particular factor may (or may not) weigh against fair use, but the other three factors might very well weigh in favor of it.
I suggest reading the 2Live Crew decision, formally called Campbell v. Acuff-Rose Music, Inc.
, 510 U.S. 569
(1994) to see how the four-factor test works. In that instance, an avowedly commercial work—a song parody that quoted extensive parts of Roy Orbison's "Oh Pretty Woman"—in a rather raunchy fashion and was reproduced as part of a platinum record (can't get much more commercial than that) was found to be fair use. Justice Souter's discussion is not
limited to parodies; it is widely considered, even in the academic community, the definitive description of weighing fair use factors.
All of that said, it's good practice
to obtain permission for anything more than a de minimis
use. It is not, however, a legal requirement, except if the publishing contract explicitly makes it so (which is, in the end, essentially unenforceable, but that's for another time).