If you need to run any distance on the roof, and you usually do, then flexible methods don't work too well, especially for avoiding rooftop temperature adders. Most of the time you need to do part of the run to the roof outside, too, and any time I need to splice costs more in time and hassle than material saved. If I'm doing flexible methods anywhere along the way, might as well do FMC and save myself splicing wires.
With that said, we've used NM plenty of times on the AC side.
Finally, yes, I think there's some bias left over from when the code effectively prohibited cables on the DC side.