I haven't driven in Europe so I don't have a good feel for how much can be accomplished in one day via car. I'm sure others can help with that. You can also get estimated driving times from ViaMichelin.com.
Caen was obliterated during the war and is now mostly modern/industrial. It has the very large Caen Memorial museum where I spent nearly an entire day, but many people find that museum too large, too expensive, too time-consuming, not sufficiently focused on WWII, etc. If that doesn't sound like your sort of thing, I definitely wouldn't choose to stay in Caen, which has only a few other points of interest. Those could be knocked off on a day-trip if need be. Caen is a major transit hub, but that's of no value to you since you plan to have a car.
Bayeux is much smaller and has a very attractive, if small, historic center. Getting in and out of town by car shouldn't be difficult, but of course you'd need to seek parking guidance from you hotel. In planning your time there (should you decide not to spend all your nights in Bayeux), I suggest allowing time for the tapestry, the cathedral, the invasion museum (2 to 3 hours would probably be enough for most people) and a walk around the historic center. I enjoyed the walking tour offered by the tourist office.
I thought it was worthwhile to spend a night or two in Rouen, which has a gorgeous, large (rebuilt) historic center and several museums. It's a city of some size, though, and I have no idea what parking and navigating would be like.
I only spent a few hours in Honfleur and wouldn't think it needed an overnight stay, but if you wanted to use it as a base for Etretat and other things in that area, it might make sense. It would be a shame to need to drive over to that area two times from Bayeux.
I haven't been to Mont-St-Michel, but south of it are two attractive historic towns I day-tripped to while staying in Rennes: Fougeres and Vitre. It was lovely to feel as if I had those places almost all to myself, because I had recently been in the very touristy St-Malo. You might have time to stop in one or both of Fougeres and Vitre on your way to or from Mont-St-Michel. They're over the line in Brittany.
Many people like St-Malo more than I did. It does have some actual sights, including a walkable wall. Dinard and Dinan are also worthwhile stops in that area.
You may find your D-Day tour leaves you wanting to see more things related to that topic.
(You wouldn't have time for everything I've mentioned.)