Yes you can go to Fatima from cruise port DIY

[jean87510]

My ship brilliance of the seas is here in lisbon from 9am today until 4pm tomorrow. We checked ship excursions plus viator and local guides. We discovered that there are buses to Fatima that leave every 30 minutes and it takes 90 minutes. Sete rios is the bus station. You need a taxi to get there. No taxis at the port will take you to sete rios bus station so you have to walk a bit to taxi stand. We had purchased our 10am ticket online and unfortunately we missed our bus by 3 minutes. No problem to exchange. Theres a red box inside where you print out your ticket. We did this not speaking any Portuguese and without help. The bus has wifi and is comfortable.  We had already downloaded our google map with all locations we wanted to see already pinned. We dropped a pin at the bus station and walked about 5-10 minutes to the shrine. Whole trip cost us 40 euros total for transportation. We had return tickets at 3pm. Bus was a little late (15minutes).

[mskaufman]

We were there on a cloudy and drizzly day this summer.  About an hour there did the trick.  Different story if it is a pilgrimage destination for you.  Otherwise, there is a lot to see in Lisbon.