As for my experience with booking tours, let's just say that I am a seasoned veteran. My husband and I were on a 12 night cruise out of Rome in September and we had a very active roll call. In many ports we had tours arranged by members of the roll call (including myself) at a fraction of the cost -- tours included a visit to the Cinque Terre and Pisa; Pompeii, Positano, and Sorrento; Athens; ancient Olympia and a local winery; etc. I've also cruised extensively in the Caribbean and done similar independent bookings and, as a member of the military, have also done lots of DIYs when pulling into ports for liberty calls.
My issue with ships tours is that they generally are larger, more expensive and provide less than the independent tours that can be arranged. We found this true of every tour that we took on our Med Cruise. Our largest group was 19 (Pompeii, Positano, Sorrento), but our smallest was 4 (Olympia and winery), while most averaged around 10.....most ship's tours appeared to be about 35.
The biggest fear most people have is that the tour operator will not get them back to the ship in time. Believe me, tour operators realize that not getting someone back to the ship would be the death of them as people would post all over cruise sites on the internet. I only deal with reputable tour operators that I've done LOTS of research on in advance to make sure that they are on the up and up.