Hi, Long Walk, welcome to the forum.
I´m not saying there´s anything wrong with buses, but if I have a choice I go on the train. Here are some of the considerations:
Frequency: There are more buses per day from Ponferrada to Madrid than trains. Weekday buses leave Ponferrada at 1:30 (am), 8:30, 9:30, 10:40, 2:30, 3:30, 5:30, 7:10 (p.m.) Trains are at 1:30 a.m. (overnight trainhotel, you can get a bed, arrives at 8 am), 6:30 am, 12:41 pm.
End point: Some of the buses make a stop at the airport -- are you heading straight home or will you be going into Madrid? If you don´t get off at the airport, they stop at the Estación which is generally out of the way and not centrally located. In fact, if I were going into Madrid, I think I would get off at the airport and take the train into Sol or wherever you are going because it´s likely to be much quicker). Trains all stop at Chamartin station. From there to the airport it´s a quick ride on a commuter train, at least if you are flying in and out of T4 (if you fly Iberia, American, British Airways, or another One World partner, you will go in and out of T4; if you fly any other airline you are at the older T1, 2, or 3 and it´s a bit more complicated to get there from Chamartin).
Duration: Pretty much the same, between 4 1/2 and 5 hours.
Price: Train may be cheaper, depending on whether you can get a good fare online. Fare sales get the train price to between 18-20€, while bus is between 30-40€
I know all of this because a friend is considering meeting me in Ponferrada to walk this summer, and we´ve been looking at transportation options.
Buen camino, Laurie