How small are we talking?
Our DD is 3 and N 8 and N 11.
I am the biggest person AGAINST the trolley, I turn adults off to it. So, my opinion may be a little jaded. But as for taking little ones...the trolley ride can be boring for the little ones, and there is one bathroom break for everyone. And it is in the middle of the tour. (We used this opportunity to escape!) If your kids are uninterested, or need a break before this...you may not want to confine yourself to the trolley tour. Just go for the aquariaum or other things.
One of the other things you will want to be aware of is the "scenery" in KW. For a 3 year old, it was no big deal...but even in the middle of the day, our BIL and SIL had a lot of explaining, or NOT explaining to do.
My advice is to head for a location like the aquarium and enjoy that!
Otherwise have a great cruise and a great trip to Key West. Shirley of THe Perfect is our resident Key West expert...maybe you want to PM her and ask her advice.