Not that I'm an expert on reading the mysterious runes of the vague information we have concerning comic sales, but aren't Ms Marvel's sales holding up fairly well?
I think Carol Danvers has a number of issues with which to contend - 1, as you say, she doesn't have a continuous history of publication, and yet 2, Carol has also been around and present for an awfully long time. So she's hit by the double whammy of being simultaneously both new and old, which is a difficulty also faced by the Inhumans. Even if her ongoing was really good - as was the case with Tom King's Vision - it probably wouldn't be sufficient to help her.
(Speaking personally, I'm just not a fan of military-themed heroes, unless they're portrayed in a partially satirical way. Therefore, Civil War 2 hasn't really damaged Carol in my eyes at least - I found her clueless authoritarianism rather amusing )