Were you to place a Rogue who had only just begun training with her powers against Captain Marvel, the fight would be pretty decidedly in the Captain's favour. Rogue's ability to take people's powers proved one of the more complicated move-sets to train with, resulting in her accidentally possessing or being possessed by people she tried to use her own powers on.
However, modern-day Rogue no longer has to worry about the issue, as the negative aspect of her powers was erased in the Messiah Complex series. Perhaps more importantly, Rogue also gained the ability to permanently take on a person's powers permanently should she be in contact with them for long enough, which currently has allowed her continual control of Wonder Man's considerable power set.
Perhaps more importantly, Rogue has also canonically defeated Captain Marvel before - albeit, during the time she went as 'Ms.Marvel' - taking both her powers and her memories the first time the two interacted.
Although Rogue and Captain Marvel are no longer outright rivals, there is still the strong suggestion that, were they to go for another round, Rogue would come out on top yet again.