Although Portugal is a small country, moving around is not the easiest. We have many options: buses, trains, barges/ferries, trams and of course cars (own, rented or shared). I will try to bring the subject closer to the interested.
Trains or CP are quite a convenient option (although sometimes they are expensive) if you are going to larger cities such as Lisbon, Porto, Coimbra, Torres Vedras or Faro. Then the stations are more or less centrally located, but within the city. Worse, if we want to reach smaller towns such as Peniche, Fatima, Albufeira, we risk a walk from a few to sometimes several kilometers to the center. More information about connections, prices and discounts can be found at: CP - how to travel
Long-distance buses: Rede, Eva, RodoNorte, RDO, reach most of the larger and smaller towns. The only problem is that many of them unfortunately require changes in Lisbon - there are no direct ones. They are sometimes cheaper than fast trains, but more expensive than regional ones. They are often faster on the spot than the trains.
Public transport: Porto and Lisbon have a well-developed metro network, plus trams, buses and ferries. If you are staying longer, it is worth considering a monthly ticket. Unfortunately, tourists have limited options: a 24h bill or a ZAPPING recharge card. More information about connections, prices and discounts can be found on the websites: Lisbon (MetroLizbona) and Porto (MetroPorto).
Cars: if we want to save time, it is definitely worth renting a car, unfortunately it is quite an expensive solution and there are the costs of highways, parking lots and the stress of the driver related to not knowing the country.