I was just in Messina and tried to take the train to Taormina. Here is what we experienced. The train station is about a 20-minute walk from the port. Just walk out of the port (which is right downtown in the center of everything), turn left and then turn left on the first main street that you come to. Continue walking until you see the bus/train station.
However, the train schedule is such that it is difficult to get to Taormina with enough time to really see/enjoy it unless your ship stays later than ours did (5pm). The latest train one could get back to the port was a little after 3pm. The bus to Taormina is a local bus and takes almost two-hours to get there after numerous stops. Folks that did the bus said it was hot, crowded and sticky.
This is one port that I would suggest that you either take one of the ship's excursions or hire a taxi to do the sights. Taxis are plentiful around the Cathedral in the center of town and were quoting 120 to 150 euro to do both attractions.
Don't discount Messina though. We had a wonderful time shopping and found a great restaurant/bar where we spent the afternoon and had a very memorable time. The Irish pub right across the street from the ship is also noteable.