Porto to Coimbra, Fatima and Tomar are easy if one is travelling by car.
I love both, but to get to Tomar by train, means getting a train to Entroncamento and then changing to a local "up-train" to Tomar!
However the only easy way to get to Fatima by public transport from any point is by Long-Distance Coach.
Although it is only 38km from Tomar to Fatima, there are only 4 daily bus services between the two on weekdays and 2 daily services on week-ends.
I have published extracts from the timetable on scribd here:
So one could get the train/bus from Porto to Coimbra, then a Rede Expressos bus to Fatima, a Rodotejo bus from Fatima to Tomar and then a train from Tomar to Lisbon.
For train info see: http://www.cp.pt
In Coimbra, have a look at this page for some of my ramblings and tips on the town:
In Tomar, I can recommend the Hotel dos Templarios.
Stayed there in August this year and it is very nice.