Your best bet is probably asking on cruise critic, but my guess is probably not for those cities. I've never done that route, so I don't have any first hand experience, but from what I've seen at places that were similar, they often don't, but it can be a mixed bag. The fact that they offer the on-your-own excursion though to me is a telling point that they're not going to offer a cheaper bus service, after all, if they did, who would use that excursion.

I've seen them offer a "cheap" bus into town center in a couple of places (hmm, I think there were one or two places they did it on the Baltic cruise I did last year, but I can't remember which they were, we took public transport instead). But in a place like Rome, they offered the on-your-own tour, and did not have any other sort of transportation (outside of other excursions).