You are right, breast milk alone is not cariogenic.
It sounds as though your dentist may be including night time breastfeeding into bottle rot diagnosis.Somehow dentists and doctors have twisted this to include breastfeeding. Yet in studies of dental enamel, breastmilk does not erode it, which leads to decay and caries. Teeth were actually placed in various solutions at a university lab study and there was zero erosion on enamel from BM, however cow's milk eroded it. AAP has stated that breastmilk is not cariogenic as well as various studies such as this one: http://www.ncbi.nlm.nih.gov/pubmed/10197331
Were you children low birth weight, preemie or did they have severe reflux?
Low birth weight and premature babies can have enamel defects which may put them at risk for decay. Per reflux, it can erode enamel leading to decay. I would imagine breastmilk is often blamed when stomach acid is the culprit.
Sucrose and heat treated starches with sucrose (cereals) are very cariogenic.
If your child teethed on hard objects and damaged enamel, chips and such, the risk of decay is increased too.
My own adecdote, my son at 11 months teethed on the metal nozzle of the garden hose and chipped enamel on two teeth (one of my regrets). Almost two years later, the brown discoloration on the tip of one is completely gone and the other is nearly gone. I still BF on demand all night.
Regarding flouride, if your local water is flouridated with at least .3 ppm flouride, your child likely does not need additional flouride (per AAP). I, like you, do not use a flouridated paste for brushing my child's teeth.
I do feel it is important to get teeth as clean as possible before bed though, so if there is any way to increase the brushing per your nursling, it may be worth it.
This is really helpful information that I have been wondering about myself. Thank you so much for sharing!