We have three days to explore southern England after a cruise? Would you recommend staying in London and doing day trips from London or would we have time to do the train and find places to stay?
Where does your ship arrive and where are you leaving from? Does the 3 days include your arrival and/or departure day? Have you been here before and is it likely you will visit again? As you are thinking about places other than London I'd guess it isn't your first visit, but please do confirm that to help people give you the best advice.
In three days you could do Salisbury, Stonehenge, Bath and the Cotswolds with a car. I don't know about trains in England anymore as I haven't been on one in 20 years, always driving. Any reason why you wouldn't do that, apart from the half hour of sheet terror at the start of driving on the left (joke, mostly)?
If you have 3 full days then I would suggest catching the rail to Salisbury, Bath or some other destination in the West Country. Find a small village and relax for a bit.