My wife and I did a cruise from Lisbon to Venice on our honeymoon, and it was my first trip to Europe (have since had fifteen others not counting business trips). I don't think it's a bad way to go, as much as I prefer traveling by land. We also did a round trip out of Athens in 2011 because I found myself with some unexpected time off. It was great because I did not have to spend a lot of time planning. The planning part is always on me, and it's very stressful. On our 2011 trip I used Rick's Mediterranean Cruise Port book which I strongly recommend.
Cruises are great for visiting places that are hard to get to, and for quick stops at places that might not otherwise merit a multi-day stay. They can be great for seeing places that are really expensive too. Or places that you might not feel like traveling to independently. I doubt whether we would have made it to Morocco or Tunisia if not on our honeymoon cruise. Sardinia, Gibraltar, Mykonos, Crete, Corfu, Palermo, Dubrovnik, Split, Kotor. These are some of the other ports that we have visited on cruises.
I don't think cruise stops in inland cites like Rome and Florence are good because as you are aware, the ship actually docks on the coast quite far from those cities, and each of those cities has such an overwhelming number of sights to see that you will leave disappointed. You may also feel like you need to purchase an expensive ship excursion (and the prices have really gone up for those). Personally I would not feel comfortable taking the train from Civitavecchia to Rome on my own, though people do it. You can research in advance which ports are close to the places you will visit. This varies a lot and even if you dock in the city that's the attraction, the port may be some distance from the actual city center. An example is Dubrovnik where we had to take a bus to get to the center. (Provided for $10 by the cruise line). A cruise also lets you scout out places for a future return visit on land. We went back to Lisbon, Seville, Gibraltar, and Venice on land after our honeymoon cruise.
Since it's your honeymoon you might want to splurge on a veranda cabin. Also choose your cruise line based upon your interests.
A big down side to a cruise is that you have limited time in port and unless it's an overnight stay, you miss out on evenings. Sometimes the time in port can be frustratingly short, as in leaving at 3 p.m. You can usually check all of this out in advance though. The cruise lines are pretty good about not forcing you into a paid excursion, but there will be ports where you have to do it. (Or at least Holland America was-- that's the one that we chose for our Europe cruises with great results).
Especially with a stay on land on one or both ends, I think a cruise can be a reasonable choice for a honeymoon.