Typically, supplements become prescription-only when they exceed a given dose. Much like ibuprofen: you can get that OTC, but there are prescription-only ibuprofen pills that are identical except for dosage. The prescription is required simply because the dosage is at a level that should have medical supervision.

I don't know if this is the case with prescription folic acid, or if there's actually something else different about them, but I suspect it's just a dosage thing.