But in TNG, every Starfleet vessel is a starship (Sisko even pretends his runabout is one in "Vortex"!), so "cruiser" has an excuse to be a Starfleet subcategory there.
Amusingly, Star Trek is almost as strict about the difference between "freighter" and "transport" as the real-world navies are. On the other hand, the TNG TM mentions "tanker", which is another civilian term. Navies don't have "tankers", they have "fuel transports" - it's air forces that have tankers (the flying sort), and armies (the people who drive tanks). Although that's nowhere as strict a thing as navies never having "freighters".