I haven't checked this forum in a while and just noticed your post. How is the napping going now?
I started a thread about this last winter. DD (3 at the time) was in a Montessori preschool that required the children rest for 1 hour. From day one DD had problems. They wouldn't let her have anything on her mat, she just had to lay there. Some days were better than others, but by February I'd had enough of the phone calls and notes home about her inability to lie still for one hour. Like you, DD hadn't been napping consistently at home for quite some time.
We ended up telling them that if they couldn't find a solution for one hour during the day for her, we would withdraw her from the school. By this point I felt like I had done everything I could to back up the teachers in helping DD learn what was expected of her. For whatever reason, this seemed to wake them up to our unhappiness, and from then on I didn't hear much about naptime anymore. I think they resorted to letting her "help" the teachers prepare things around the room while the other kids were resting.
We ended up moving out of state at the end of the school year and DD is enrolled in another Montessori program now. They do not have mandatory rest time, just an additional work cycle. DD is thrilled and the whole experience seems much more positive now.
I encourage you to have discussions with the teachers and the director about what they expect and what you think is appropriate. If they have any suggestions of things you could talk about with your son at home or things you could try on the weekends, give it a try. I will say that looking back I wish we had either moved her to another room or another school sooner. After months of hassle over such a small part of their day, it definitely changed DD's experience in an unpleasant way. She dreaded naptime and really began to believe she was difficult in the eyes of her teachers.
I hope things are getting better for you. Hang in there.