Well, the question is, when does legitimate "puffery" and salesmanship become inducing fear?
Those of you who follow my often inane comments know that I always say that you have to decide what your level of comfort it. It is not only legitimate but good customer care for the cruise lines to make clear just what the choices are. Then people can decide.
Ship's excursions are convenient, easy to book, well guided and supervised, and usually very much on time. They are an excellent choice for many people, not because they are afraid but because of their good value to benefit ratio.
OTOH independent excursions can also be excellent but do have that small element of risk. In our 40+ cruises, we have been the last passengers up the gangway twice due to small glitches with independent operators. We balance the risks against the benefits and the value and decide which to do. For the ship to point this out is not really fear-mongering, just good merchandising IMAO.
I also feel that some of the more vocal advocates of always booking independent exaggerate the cost savings possible. In our experience, independent excursions are rarely much of a savings over the cruise lines trips, and we almost never choose an independent excursion because of some ephemeral savings.