Was this an isolated question or was it associated with a specific configuration and transformer tap conductor length? In particular, 240.21(B)(3) addresses taps supplying a transformer where the primary plus secondary length is not over 25 feet and clause (4) requires a raceway or other approved means. That's why NM cannot be used in that situation (unless in a raceway).
In fact, if you look at 240.21(B)(2 thru 4) each of the situations described has a clause requiring tap conductors to be in a raceway or other approved means. 240.21(B)(1) is slightly different, but still has a raceway requirement.
A suggestion - if you're only using the NEC manual for your studies, try to obtain a copy of the NEC Handbook. It contains the NEC manual and its purpose is to illustrate and help clarify NEC "gobbledygook" (at which it's only partially successful - you'll still have bald patches from scratching your head over NEC meanings.)
